Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xcu Working: n-9-19.cluster.ucsf.bkslab.org:/scratch/xiaobo/335759/xcu-8058115.73 Result: /scratch/xiaobo/335759/xcu-8058115.73 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xcu Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/inputs/xcu mkdir: created directory `/scratch/xiaobo/335759' mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73' /scratch/xiaobo/335759/xcu-8058115.73 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working' mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/protonate' Storing results in /scratch/xiaobo/335759/xcu-8058115.73/finished Working in /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 /scratch/xiaobo/335759/xcu-8058115.73/working/protonate /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Using inputs as protomers/tautomers. No processing done 452 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/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Bulk generating 3D conformations all protomers in /scratch/xiaobo/335759/xcu-8058115.73/working/3D mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/335759/xcu-8058115.73/working/protonate/xcu-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 ZINC000552689526 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building' mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000552689526 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/1 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(Cl)ccc1CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000552689526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552689526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000552689526 none Cc1cc(Cl)ccc1CN1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 16, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 17, 11, 11, 11, 11, 5, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 28, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 5, 5, 5, 5, 5, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000552689526 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/finished' Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526/0.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552689526 Building ZINC000130809493 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000130809493 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/2 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/3 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/3' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/4 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/4' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/5 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/5' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000130809493 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 Building ZINC000130809493 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000130809493 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 2) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 3) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 4) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 5) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000130809493 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 Building ZINC000130809493 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000130809493 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 2) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 3) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 4) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 5) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000130809493 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 Building ZINC000130809493 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000130809493 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 2) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 3) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 9, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 19, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 19, 19, 19, 19, 19, 19, 50, 50, 50, 19, 19, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 4) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 5) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1) `ZINC000130809493.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000130809493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000130809493 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2CCCN(c3cccnn3)C2)cc1 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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 5, 10, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 22, 22, 22, 22, 22, 22, 50, 50, 50, 22, 22, 4, 4] 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000130809493 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000130809493 Building ZINC000162689198 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162689198 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/6 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1) `ZINC000162689198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162689198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000162689198 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 24, 24, 24, 35, 35, 35, 35, 35, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 24, 24, 24, 35, 35, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/7 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1) `ZINC000162689198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162689198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000162689198 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 24, 24, 24, 37, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 24, 24, 24, 37, 37, 37, 37, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000162689198 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 Building ZINC000162689198 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000162689198 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 6) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1) `ZINC000162689198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000162689198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000162689198 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 24, 24, 24, 35, 35, 35, 35, 35, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 24, 24, 24, 35, 35, 35, 35, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 7) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1) `ZINC000162689198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000162689198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000162689198 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2ccccn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 6, 13, 13, 13, 13, 24, 24, 24, 37, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 24, 24, 24, 37, 37, 37, 37, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000162689198 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000162689198 Building ZINC000107325745 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325745 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/8 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/9 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/10 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/10' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/11 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/11' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325745 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 Building ZINC000107325745 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325745 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 8) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 9) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 10) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 11) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325745 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 Building ZINC000107325745 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325745 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 8) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 9) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 10) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 11) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325745 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 Building ZINC000107325745 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325745 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 8) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 9) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 5, 12, 12, 12, 12, 40, 50, 50, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 10) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 11) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCN(C[C@H]3CCCCN3C)CC2)cc1) `ZINC000107325745.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325745 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 2, 5, 5, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 37, 50, 50, 50, 50, 50, 50, 50, 13, 13, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 13, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325745 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325745 Building ZINC000107325748 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325748 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/12 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/13 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/14 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/14' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/15 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/15' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325748 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 Building ZINC000107325748 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325748 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 12) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 13) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 14) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 15) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325748 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 Building ZINC000107325748 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325748 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 12) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 13) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 14) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 15) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325748 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 Building ZINC000107325748 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000107325748 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 12) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 13) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 4, 12, 12, 12, 12, 32, 48, 48, 48, 48, 48, 48, 48, 12, 12, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 16, 16, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 14) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 15) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1) `ZINC000107325748.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000107325748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000107325748 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C[C@@H]3CCCCN3C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 5, 13, 13, 13, 13, 36, 47, 47, 47, 47, 47, 47, 47, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 13, 13, 13, 13, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000107325748 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000107325748 Building ZINC000552922577 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552922577 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/16 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1CC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000552922577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552922577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000552922577 none COC(=O)c1ccccc1CC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 30, 17, 17, 16, 17, 17, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 30, 30, 30, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/17 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000552922577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552922577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000552922577 none COC(=O)c1ccccc1CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 34, 21, 21, 21, 21, 21, 12, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 21, 21, 21, 21, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000552922577 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 Building ZINC000552922577 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000552922577 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 16) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/16: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1CC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000552922577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000552922577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000552922577 none COC(=O)c1ccccc1CC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 17, 30, 17, 17, 16, 17, 17, 10, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 30, 30, 30, 17, 17, 17, 17, 10, 10, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 3, 3, 3, 3] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 17) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1ccccc1CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000552922577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000552922577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000552922577 none COC(=O)c1ccccc1CC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 21, 34, 21, 21, 21, 21, 21, 12, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 21, 21, 21, 21, 12, 12, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000552922577 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000552922577 Building ZINC000731230024 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731230024 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/18 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731230024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731230024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731230024 none CC(C)n1c(S)nnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 18, 18, 18, 18, 18, 18, 18, 54, 11, 11, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/19 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731230024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731230024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731230024 none CC(C)n1c(S)nnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 12, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 20, 20, 20, 20, 20, 20, 20, 60, 12, 12, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731230024 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 Building ZINC000731230024 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731230024 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 18) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731230024.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731230024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731230024 none CC(C)n1c(S)nnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 11, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 18, 18, 18, 18, 18, 18, 18, 54, 11, 11, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 19) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731230024.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731230024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731230024 none CC(C)n1c(S)nnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 20, 20, 20, 20, 20, 20, 12, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 7, 20, 20, 20, 20, 20, 20, 20, 60, 12, 12, 4, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 146 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731230024 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731230024 Building ZINC000163061068 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163061068 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/20 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163061068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061068 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 28, 28, 28, 28, 28, 28, 47, 47, 47, 47, 28, 28, 6, 6, 6, 6, 6, 6, 6, 3, 28, 28, 28, 28, 28, 28, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/21 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163061068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061068 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 30, 5, 5, 5, 5, 5, 5, 5, 4, 30, 30, 30, 30, 30, 30, 46, 46, 5, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000163061068 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 Building ZINC000163061068 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163061068 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 20) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/20: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163061068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061068 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 28, 28, 28, 28, 28, 28, 47, 47, 47, 47, 28, 28, 6, 6, 6, 6, 6, 6, 6, 3, 28, 28, 28, 28, 28, 28, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 21) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163061068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061068 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 5, 5, 1, 1, 1, 1, 4, 4, 7, 30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 30, 5, 5, 5, 5, 5, 5, 5, 4, 30, 30, 30, 30, 30, 30, 46, 46, 5, 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]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000163061068 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061068 Building ZINC000163061190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163061190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/22 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163061190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061190 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 9, 30, 30, 30, 30, 30, 30, 47, 47, 47, 47, 30, 30, 5, 5, 5, 5, 5, 5, 5, 3, 30, 30, 30, 30, 30, 30, 47, 47, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/23 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163061190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061190 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 9, 30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 30, 6, 6, 6, 6, 6, 6, 6, 3, 30, 30, 30, 30, 30, 30, 46, 46, 6, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000163061190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 Building ZINC000163061190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000163061190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 22) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000163061190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061190 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 1, 5, 5, 1, 1, 1, 1, 3, 3, 9, 30, 30, 30, 30, 30, 30, 47, 47, 47, 47, 30, 30, 5, 5, 5, 5, 5, 5, 5, 3, 30, 30, 30, 30, 30, 30, 47, 47, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 23) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/23: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1) `ZINC000163061190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000163061190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000163061190 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCCN(CC(F)(F)F)C2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 9, 30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 30, 30, 6, 6, 6, 6, 6, 6, 6, 3, 30, 30, 30, 30, 30, 30, 46, 46, 6, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000163061190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000163061190 Building ZINC000268356566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268356566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/24 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000268356566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268356566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000268356566 none CN(C)C(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 19, 50, 16, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 19, 19, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/25 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/25' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000268356566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268356566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000268356566 none CN(C)C(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 15, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 16, 16, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268356566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 Building ZINC000268356566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268356566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 24) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/24: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000268356566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268356566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000268356566 none CN(C)C(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 19, 50, 16, 8, 8, 8, 8, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 19, 19, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 164 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 25) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/25: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000268356566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268356566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000268356566 none CN(C)C(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 16, 50, 15, 6, 6, 6, 6, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 50, 16, 16, 15, 15, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 150 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268356566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268356566 Building ZINC000553140244 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553140244 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/26 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553140244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140244 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 18, 18, 18, 27, 27, 27, 27, 3, 4, 4, 8, 8, 8, 8, 8, 4, 3, 3, 3, 3, 3, 3, 8, 8, 18, 27, 27, 3, 3, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/27 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/27' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553140244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140244 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 13, 13, 21, 21, 21, 21, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 8, 8, 13, 21, 21, 3, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553140244 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 Building ZINC000553140244 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553140244 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 26) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553140244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140244 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 18, 18, 18, 27, 27, 27, 27, 3, 4, 4, 8, 8, 8, 8, 8, 4, 3, 3, 3, 3, 3, 3, 8, 8, 18, 27, 27, 3, 3, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 27) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553140244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140244 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 13, 13, 21, 21, 21, 21, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 8, 8, 13, 21, 21, 3, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553140244 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140244 Building ZINC000553140245 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553140245 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/28 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553140245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140245 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 13, 13, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 8, 8, 13, 22, 22, 3, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/29 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553140245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140245 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 7, 16, 16, 16, 25, 25, 25, 25, 3, 4, 4, 8, 8, 8, 8, 8, 4, 3, 3, 3, 3, 3, 3, 7, 7, 16, 25, 25, 3, 3, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553140245 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 Building ZINC000553140245 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553140245 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 28) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553140245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140245 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens 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, 3, 3, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 8, 13, 13, 13, 22, 22, 22, 22, 3, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 8, 8, 13, 22, 22, 3, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 29) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/29: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1) `ZINC000553140245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553140245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000553140245 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CNC(=O)CC(F)(F)F)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 15, 15, 15, 5, 1, 8, 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, 9, 8, 10, 11, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 7, 16, 16, 16, 25, 25, 25, 25, 3, 4, 4, 8, 8, 8, 8, 8, 4, 3, 3, 3, 3, 3, 3, 7, 7, 16, 25, 25, 3, 3, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553140245 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553140245 Building ZINC000470125152 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470125152 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/30 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470125152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125152 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 4, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/31 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470125152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125152 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 20, 4, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470125152 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 Building ZINC000470125152 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470125152 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 30) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/30: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470125152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125152 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 29, 29, 29, 29, 29, 29, 29, 29, 19, 19, 19, 4, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 31) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/31: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470125152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125152 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 20, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 26, 26, 26, 26, 26, 26, 26, 26, 20, 20, 20, 4, 3, 3, 3, 3, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470125152 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125152 Building ZINC000470125155 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470125155 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/32 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470125155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125155 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 8, 21, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 21, 4, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/33 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470125155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125155 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 19, 4, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470125155 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 Building ZINC000470125155 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470125155 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 32) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470125155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125155 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 8, 21, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 21, 4, 3, 3, 3, 3, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 33) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2) `ZINC000470125155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470125155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC000470125155 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1ccc2c(c1)CCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 30, 30, 30, 30, 30, 30, 30, 30, 19, 19, 19, 4, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470125155 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470125155 Building ZINC000553144815 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553144815 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/34 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553144815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144815 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 15, 21, 21, 21, 15, 15, 6, 6, 6, 17, 17, 17, 6, 6, 3, 8, 8, 8, 21, 21, 21, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/35 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/35' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553144815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144815 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 5, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 17, 25, 25, 25, 17, 17, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 25, 25, 25, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553144815 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 Building ZINC000553144815 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553144815 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 34) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553144815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144815 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 15, 21, 21, 21, 15, 15, 6, 6, 6, 17, 17, 17, 6, 6, 3, 8, 8, 8, 21, 21, 21, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 35) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553144815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144815 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 5, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 17, 25, 25, 25, 17, 17, 6, 6, 6, 16, 16, 16, 6, 6, 3, 8, 8, 8, 25, 25, 25, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553144815 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144815 Building ZINC000553144816 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553144816 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/36 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553144816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144816 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 16, 24, 24, 24, 16, 16, 6, 6, 6, 13, 13, 13, 6, 6, 2, 6, 6, 6, 24, 24, 24, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/37 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553144816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144816 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 20, 20, 20, 14, 14, 6, 6, 6, 16, 16, 16, 6, 6, 3, 7, 7, 7, 20, 20, 20, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553144816 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 Building ZINC000553144816 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553144816 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 36) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144816.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553144816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144816 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 2, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 16, 24, 24, 24, 16, 16, 6, 6, 6, 13, 13, 13, 6, 6, 2, 6, 6, 6, 24, 24, 24, 16, 16, 16, 16, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 130 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 37) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl) `ZINC000553144816.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553144816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000553144816 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)C2(S(C)(=O)=O)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 14, 5, 11, 11, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 14, 20, 20, 20, 14, 14, 6, 6, 6, 16, 16, 16, 6, 6, 3, 7, 7, 7, 20, 20, 20, 14, 14, 14, 14, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553144816 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553144816 Building ZINC000109661710 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000109661710 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/38 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/39 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/40 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/40' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/41 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/41' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000109661710 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 Building ZINC000109661710 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000109661710 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 38) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 39) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 40) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 41) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000109661710 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 Building ZINC000109661710 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000109661710 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 38) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 39) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 40) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 41) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000109661710 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 Building ZINC000109661710 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000109661710 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 38) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 39) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 29, 29, 13, 5, 5, 5, 5, 5, 4, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 29, 29, 38, 38, 38, 38, 38, 29, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 29] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 40) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 41) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1) `ZINC000109661710.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000109661710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000109661710 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 28, 28, 14, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 28, 28, 35, 35, 35, 35, 35, 28, 14, 14, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 28] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000109661710 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000109661710 Building ZINC000553178747 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553178747 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/42 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1) `ZINC000553178747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553178747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000553178747 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7] 0 hydrogens 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, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 13, 13, 9, 9, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/43 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1) `ZINC000553178747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553178747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000553178747 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7] 0 hydrogens 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, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 13, 13, 9, 9, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553178747 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 Building ZINC000553178747 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553178747 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 42) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1) `ZINC000553178747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553178747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000553178747 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7] 0 hydrogens 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, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 13, 13, 9, 9, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 43) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1) `ZINC000553178747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553178747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000553178747 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)C(=O)c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 11, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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, 7] 0 hydrogens 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, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 33, 50, 50, 50, 50, 50, 50, 50, 50, 33, 17, 17, 13, 13, 9, 9, 2, 2, 2, 2, 2, 50, 50, 50, 50] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553178747 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553178747 Building ZINC000087563171 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000087563171 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/44 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000087563171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563171 none CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/45 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000087563171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563171 none CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 4, 9, 12, 12, 11, 12, 12, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000087563171 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 Building ZINC000087563171 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000087563171 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 44) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000087563171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563171 none CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 25, 25, 25, 25, 25, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 45) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000087563171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563171 none CCc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 8, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 8, 4, 9, 12, 12, 11, 12, 12, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000087563171 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563171 Building ZINC000087563172 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000087563172 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/46 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000087563172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563172 none CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/47 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000087563172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563172 none CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000087563172 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 Building ZINC000087563172 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000087563172 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 46) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/46: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000087563172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563172 none CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 28, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 47) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/47: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000087563172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000087563172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000087563172 none CCc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 12, 12, 8, 24, 24, 24, 24, 24, 8, 8, 8, 8, 8, 8, 4, 8, 12, 12, 8, 12, 12, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000087563172 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000087563172 Building ZINC000553257518 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553257518 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/48 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000553257518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553257518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000553257518 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 28, 28, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/49 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000553257518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553257518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000553257518 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553257518 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 Building ZINC000553257518 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553257518 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 48) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/48: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000553257518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553257518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000553257518 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 14, 14, 14, 14, 28, 28, 28, 28, 14, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 28, 28, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 49) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/49: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000553257518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553257518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000553257518 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 14, 14, 14, 14, 26, 26, 26, 26, 14, 14, 14, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553257518 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553257518 Building ZINC000455887117 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887117 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/50 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887117 none CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 17, 34, 34, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 16, 16, 16, 7, 7, 17, 17, 102, 6, 6, 6, 6, 6, 6, 6, 7, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 227 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/51 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887117 none CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 22, 36, 36, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 22, 22, 108, 4, 4, 4, 4, 4, 4, 4, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887117 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 Building ZINC000455887117 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887117 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 50) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/50: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887117 none CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 7, 7, 7, 7, 7, 17, 34, 34, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 16, 16, 16, 7, 7, 17, 17, 102, 6, 6, 6, 6, 6, 6, 6, 7, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 227 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 51) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/51: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887117 none CO[C@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 22, 36, 36, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 22, 22, 108, 4, 4, 4, 4, 4, 4, 4, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 257 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887117 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887117 Building ZINC000455887118 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887118 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/52 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887118 none CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 20, 33, 33, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 10, 17, 17, 17, 10, 10, 20, 20, 99, 4, 5, 5, 4, 5, 5, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/53 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887118 none CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 18, 35, 35, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 9, 15, 15, 15, 9, 9, 18, 18, 105, 6, 7, 7, 6, 7, 7, 6, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887118 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 Building ZINC000455887118 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887118 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 52) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887118 none CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 20, 33, 33, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 10, 17, 17, 17, 10, 10, 20, 20, 99, 4, 5, 5, 4, 5, 5, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 228 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 53) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887118 none CO[C@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 18, 35, 35, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 9, 15, 15, 15, 9, 9, 18, 18, 105, 6, 7, 7, 6, 7, 7, 6, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 236 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887118 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887118 Building ZINC000455887126 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887126 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/54 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887126 none CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 20, 36, 36, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 15, 15, 15, 10, 10, 20, 20, 108, 6, 6, 6, 6, 6, 6, 6, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/55 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/55' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887126 none CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 20, 36, 36, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 10, 17, 17, 17, 10, 10, 20, 20, 108, 4, 5, 5, 4, 5, 5, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887126 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 Building ZINC000455887126 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887126 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 54) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887126 none CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 20, 36, 36, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 15, 15, 15, 10, 10, 20, 20, 108, 6, 6, 6, 6, 6, 6, 6, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 238 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 55) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887126 none CO[C@@H]1C[C@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 20, 36, 36, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 10, 17, 17, 17, 10, 10, 20, 20, 108, 4, 5, 5, 4, 5, 5, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 245 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887126 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887126 Building ZINC000455887128 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887128 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/56 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887128 none CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 23, 37, 37, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 23, 23, 111, 4, 4, 4, 4, 4, 4, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 262 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/57 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887128 none CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 17, 33, 33, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 8, 16, 16, 16, 8, 8, 17, 17, 99, 6, 7, 7, 6, 7, 7, 6, 8, 8] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887128 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 Building ZINC000455887128 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455887128 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 56) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887128.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455887128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887128 none CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 10, 10, 10, 10, 10, 10, 23, 37, 37, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 23, 23, 111, 4, 4, 4, 4, 4, 4, 4, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 262 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 57) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455887128.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455887128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455887128 none CO[C@@H]1C[C@@H](CC(=O)O)N(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.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', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 7, 5, 1, 11, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 5, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 17, 33, 33, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 8, 16, 16, 16, 8, 8, 17, 17, 99, 6, 7, 7, 6, 7, 7, 6, 8, 8] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 224 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455887128 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455887128 Building ZINC000455897191 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455897191 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/58 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455897191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897191 none COC[C@@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 27, 12, 12, 12, 19, 19, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 32, 27, 27, 57, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 12, 12] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 182 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/59 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455897191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897191 none COC[C@@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 27, 10, 10, 10, 15, 15, 10, 10, 2, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 10, 35, 35, 35, 27, 27, 45, 10, 10, 10, 10, 6, 8, 8, 6, 8, 8, 6, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455897191 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 Building ZINC000455897191 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455897191 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 58) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/58: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455897191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897191 none COC[C@@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 27, 12, 12, 12, 19, 19, 12, 12, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 32, 32, 32, 27, 27, 57, 12, 12, 12, 12, 4, 4, 4, 4, 4, 4, 4, 12, 12] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 182 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 59) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/59: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455897191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897191 none COC[C@@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 27, 10, 10, 10, 15, 15, 10, 10, 2, 1, 3, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 10, 35, 35, 35, 27, 27, 45, 10, 10, 10, 10, 6, 8, 8, 6, 8, 8, 6, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 183 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455897191 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897191 Building ZINC000455897192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455897192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/60 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455897192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897192 none COC[C@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 25, 11, 11, 11, 20, 20, 11, 11, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 30, 30, 30, 25, 25, 60, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/61 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455897192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897192 none COC[C@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 29, 10, 10, 10, 18, 18, 10, 10, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 33, 33, 33, 29, 29, 54, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455897192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 Building ZINC000455897192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455897192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 60) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455897192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897192 none COC[C@]1(C(=O)O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 25, 11, 11, 11, 20, 20, 11, 11, 2, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 30, 30, 30, 25, 25, 60, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 11, 11] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 61) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000455897192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455897192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000455897192 none COC[C@]1(C(=O)O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', '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, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 5, 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] 1 hydrogens 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, 29, 10, 10, 10, 18, 18, 10, 10, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 33, 33, 33, 29, 29, 54, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 10, 10] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 185 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455897192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455897192 Building ZINC000455893347 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455893347 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/62 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/62' -> `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](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455893347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893347 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 40, 40, 40, 40, 40, 40, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 40, 40, 40, 40, 54] 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]) total number of confs: 215 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/63 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/63' -> `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](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455893347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893347 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 26, 41, 41, 41, 41, 41, 41, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 26, 26, 41, 41, 41, 41, 60] 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]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455893347 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 Building ZINC000455893347 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455893347 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 62) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455893347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893347 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 40, 40, 40, 40, 40, 40, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 40, 40, 40, 40, 54] 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]) total number of confs: 215 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 63) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455893347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893347 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 26, 41, 41, 41, 41, 41, 41, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 26, 26, 41, 41, 41, 41, 60] 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]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455893347 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893347 Building ZINC000455893349 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455893349 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/64 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/64' -> `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](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455893349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893349 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 26, 41, 41, 41, 41, 41, 41, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 26, 26, 41, 41, 41, 41, 60] 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]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/65 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/65' -> `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](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455893349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893349 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 40, 40, 40, 40, 40, 40, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 40, 40, 40, 40, 54] 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]) total number of confs: 215 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455893349 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 Building ZINC000455893349 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000455893349 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 64) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/64: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000455893349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893349 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 26, 41, 41, 41, 41, 41, 41, 14, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 26, 26, 41, 41, 41, 41, 60] 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]) total number of confs: 219 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 65) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/65: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O) `ZINC000455893349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000455893349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000455893349 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](Cc1cccc(Cl)c1)C(=O)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 1, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 40, 40, 40, 40, 40, 40, 12, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 25, 25, 40, 40, 40, 40, 54] 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]) total number of confs: 215 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000455893349 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000455893349 Building ZINC000115126102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115126102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/66 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)ccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000115126102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115126102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000115126102 none COc1cc(F)ccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 26, 31, 31, 31, 11, 11, 11, 11, 6, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 31, 31, 31, 31, 31, 31, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/67 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/67' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)ccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000115126102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115126102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000115126102 none COc1cc(F)ccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 6, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000115126102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 Building ZINC000115126102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115126102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 66) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)ccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000115126102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115126102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000115126102 none COc1cc(F)ccc1N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 26, 31, 31, 31, 11, 11, 11, 11, 6, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 31, 31, 31, 31, 31, 31, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 67) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(F)ccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000115126102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115126102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000115126102 none COc1cc(F)ccc1N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 6, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000115126102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000115126102 Building ZINC000553476416 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553476416 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/68 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553476416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476416 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 3, 12, 3, 1, 3, 1, 1, 1, 5, 5, 1, 4, 5, 5, 12, 29, 49, 49, 49, 29, 29, 12, 12, 12, 3, 5, 5, 5, 5, 49, 49, 49, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 221 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/69 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553476416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476416 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [14, 5, 14, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 14, 34, 46, 46, 46, 34, 34, 14, 14, 14, 5, 4, 4, 4, 4, 46, 46, 46, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553476416 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 Building ZINC000553476416 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553476416 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 68) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553476416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476416 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 3, 12, 3, 1, 3, 1, 1, 1, 5, 5, 1, 4, 5, 5, 12, 29, 49, 49, 49, 29, 29, 12, 12, 12, 3, 5, 5, 5, 5, 49, 49, 49, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 221 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 69) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553476416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476416 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [14, 5, 14, 5, 1, 5, 1, 1, 1, 4, 4, 1, 4, 4, 4, 14, 34, 46, 46, 46, 34, 34, 14, 14, 14, 5, 4, 4, 4, 4, 46, 46, 46, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553476416 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476416 Building ZINC000553476417 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553476417 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/70 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553476417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476417 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 5, 13, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 47, 47, 47, 30, 30, 13, 13, 13, 5, 3, 3, 3, 3, 47, 47, 47, 30, 30, 30, 30] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/71 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553476417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476417 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 3, 12, 3, 1, 3, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 29, 49, 49, 49, 29, 29, 12, 12, 12, 3, 5, 5, 5, 5, 49, 49, 49, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 222 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553476417 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 Building ZINC000553476417 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553476417 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 70) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476417.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553476417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476417 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [13, 5, 13, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 30, 47, 47, 47, 30, 30, 13, 13, 13, 5, 3, 3, 3, 3, 47, 47, 47, 30, 30, 30, 30] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 194 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 71) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1) `ZINC000553476417.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553476417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553476417 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 11, 11, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [12, 3, 12, 3, 1, 3, 1, 1, 1, 5, 5, 1, 5, 5, 5, 12, 29, 49, 49, 49, 29, 29, 12, 12, 12, 3, 5, 5, 5, 5, 49, 49, 49, 29, 29, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 222 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553476417 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553476417 Building ZINC000268724962 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268724962 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/72 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1) `ZINC000268724962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268724962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724962 none CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 8, 8, 8, 7, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 8, 8, 8, 8, 24, 24, 24, 8, 8, 8, 8, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/73 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1) `ZINC000268724962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268724962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724962 none CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 22, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 8, 8, 8, 8, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268724962 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 Building ZINC000268724962 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268724962 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 72) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1) `ZINC000268724962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268724962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724962 none CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 24, 8, 8, 8, 7, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 8, 8, 8, 8, 24, 24, 24, 8, 8, 8, 8, 2, 2, 2, 7, 7, 3, 7, 7, 2, 2, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 85 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 73) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1) `ZINC000268724962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268724962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724962 none CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 8, 22, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 8, 8, 8, 8, 22, 22, 22, 8, 8, 8, 8, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268724962 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724962 Building ZINC000268724963 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268724963 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/74 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1) `ZINC000268724963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268724963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724963 none CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 9, 9, 9, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 9, 9, 9, 9, 21, 21, 21, 9, 9, 9, 9, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/75 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1) `ZINC000268724963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268724963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724963 none CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268724963 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 Building ZINC000268724963 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268724963 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 74) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/74: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1) `ZINC000268724963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268724963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724963 none CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 21, 9, 9, 9, 9, 2, 9, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 9, 9, 9, 9, 21, 21, 21, 9, 9, 9, 9, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 81 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 75) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/75: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1) `ZINC000268724963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268724963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000268724963 none CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', '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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 9, 23, 9, 9, 9, 8, 2, 8, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 9, 9, 9, 9, 23, 23, 23, 9, 9, 9, 9, 2, 2, 2, 7, 7, 2, 7, 7, 2, 2, 2, 9, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268724963 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268724963 Building ZINC000268738190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/76 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/76' -> `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)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000268738190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738190 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 7, 8, 8, 8, 8, 8, 8, 8, 14, 27, 27, 27, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 81, 44, 44, 44] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/77 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/77' -> `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)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000268738190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738190 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 11, 22, 22, 22, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 66, 34, 34, 34] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 Building ZINC000268738190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 76) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000268738190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738190 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 7, 8, 8, 8, 8, 8, 8, 8, 14, 27, 27, 27, 44, 44, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 14, 14, 81, 44, 44, 44] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 77) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000268738190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738190 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 11, 22, 22, 22, 34, 34, 34, 34, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 66, 34, 34, 34] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 180 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738190 Building ZINC000268738192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/78 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/78' -> `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)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000268738192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738192 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 15, 15, 75, 34, 34, 34] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/79 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/79' -> `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)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000268738192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738192 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 18, 32, 32, 32, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 18, 18, 96, 45, 45, 45] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 Building ZINC000268738192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 78) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000268738192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738192 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 34, 34, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 6, 15, 15, 75, 34, 34, 34] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 79) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/79: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000268738192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738192 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 18, 32, 32, 32, 45, 45, 45, 45, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 18, 18, 96, 45, 45, 45] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 251 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738192 Building ZINC000268738194 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738194 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/80 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/80' -> `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)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000268738194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738194 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 19, 33, 33, 33, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 19, 19, 99, 46, 46, 46] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 260 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/81 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/81' -> `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)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000268738194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738194 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 15, 15, 75, 33, 33, 33] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738194 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 Building ZINC000268738194 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738194 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 80) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000268738194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738194 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 19, 33, 33, 33, 46, 46, 46, 46, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 19, 19, 99, 46, 46, 46] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 260 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 81) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000268738194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738194 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 6, 6, 6, 15, 25, 25, 25, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 15, 15, 75, 33, 33, 33] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738194 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738194 Building ZINC000268738198 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738198 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/82 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/82' -> `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)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000268738198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738198 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 10, 21, 21, 21, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 63, 33, 33, 33] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/83 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/83' -> `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)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000268738198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738198 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 5, 7, 8, 8, 8, 8, 8, 8, 8, 15, 27, 27, 27, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 15, 15, 81, 42, 42, 42] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738198 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 Building ZINC000268738198 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000268738198 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 82) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/82: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000268738198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000268738198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738198 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 10, 21, 21, 21, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 63, 33, 33, 33] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 83) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/83: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000268738198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000268738198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000268738198 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 4, 4, 1, 1, 1, 2, 5, 7, 8, 8, 8, 8, 8, 8, 8, 15, 27, 27, 27, 42, 42, 42, 42, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 15, 15, 81, 42, 42, 42] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000268738198 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000268738198 Building ZINC000111417247 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111417247 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/84 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1) `ZINC000111417247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111417247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111417247 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1 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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 21, 49, 49, 49, 49, 49, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 21, 21, 49, 49, 49, 49, 8, 8, 8, 8, 4, 4] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/85 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1) `ZINC000111417247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111417247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111417247 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1 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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 19, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 19, 19, 50, 50, 50, 50, 7, 7, 7, 7, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000111417247 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 Building ZINC000111417247 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000111417247 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 84) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/84: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1) `ZINC000111417247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000111417247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111417247 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1 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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 4, 8, 8, 8, 8, 21, 49, 49, 49, 49, 49, 8, 8, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 21, 21, 49, 49, 49, 49, 8, 8, 8, 8, 4, 4] 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: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 85) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/85: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1) `ZINC000111417247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000111417247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000111417247 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3cnc(C)s3)CC2)cc1 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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 7, 7, 7, 7, 19, 50, 50, 50, 50, 50, 7, 7, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 19, 19, 50, 50, 50, 50, 7, 7, 7, 7, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000111417247 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000111417247 Building ZINC000131819570 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000131819570 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/86 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1) `ZINC000131819570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000131819570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000131819570 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 22, 37, 37, 37, 37, 37, 50, 50, 50, 50, 37, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 22, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 4, 4] 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, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/87 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1) `ZINC000131819570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000131819570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000131819570 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 22, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 22, 22, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000131819570 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 Building ZINC000131819570 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000131819570 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 86) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/86: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1) `ZINC000131819570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000131819570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000131819570 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 22, 37, 37, 37, 37, 37, 50, 50, 50, 50, 37, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 22, 22, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 4, 4] 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, 46, 47]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 87) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/87: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1) `ZINC000131819570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000131819570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000131819570 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2cccc(C(=O)N(C)C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 10, 22, 38, 38, 38, 38, 38, 50, 50, 50, 50, 38, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 22, 22, 38, 38, 38, 50, 50, 50, 50, 50, 50, 38, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000131819570 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000131819570 Building ZINC000553584653 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553584653 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/88 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O) `ZINC000553584653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553584653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584653 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/89 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O) `ZINC000553584653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553584653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584653 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553584653 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 Building ZINC000553584653 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553584653 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 88) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O) `ZINC000553584653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553584653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584653 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 22, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 89) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O) `ZINC000553584653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553584653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584653 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553584653 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584653 Building ZINC000553584654 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553584654 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/90 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O) `ZINC000553584654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553584654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584654 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/91 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O) `ZINC000553584654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553584654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584654 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553584654 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 Building ZINC000553584654 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553584654 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 90) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O) `ZINC000553584654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553584654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584654 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 91) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O) `ZINC000553584654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553584654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000553584654 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCCN1S(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 8, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 20, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49, 2, 2, 2, 2, 2, 2, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553584654 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553584654 Building ZINC000456130994 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456130994 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/92 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456130994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456130994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000456130994 none COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 10, 22, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 3, 7, 8, 8, 7, 8, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/93 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456130994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456130994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000456130994 none COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 12, 24, 12, 12, 12, 12, 12, 12, 6, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 8, 8, 6, 8, 8, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456130994 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 Building ZINC000456130994 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456130994 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 92) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456130994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456130994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000456130994 none COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 10, 22, 10, 10, 10, 10, 10, 10, 5, 10, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 22, 22, 22, 10, 10, 10, 10, 10, 10, 10, 10, 3, 7, 8, 8, 7, 8, 8, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 93) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456130994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456130994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000456130994 none COC(=O)[C@@H]1CCCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 12, 24, 12, 12, 12, 12, 12, 12, 6, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 4, 6, 8, 8, 6, 8, 8, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456130994 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456130994 Building ZINC000731440460 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731440460 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/94 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731440460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731440460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000731440460 none CC(C)n1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 15, 13, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 24, 24, 24, 24, 72, 15, 15, 13, 13, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/95 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731440460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731440460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000731440460 none CC(C)n1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 24, 23, 23, 23, 23, 23, 16, 14, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 24, 24, 24, 24, 69, 16, 16, 14, 14, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731440460 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 Building ZINC000731440460 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731440460 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 94) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731440460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731440460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000731440460 none CC(C)n1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 15, 13, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 24, 24, 24, 24, 72, 15, 15, 13, 13, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 181 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 95) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731440460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731440460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000731440460 none CC(C)n1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 24, 23, 23, 23, 23, 23, 16, 14, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 24, 24, 24, 24, 24, 24, 24, 69, 16, 16, 14, 14, 2, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 185 number of broken/clashed sets: 101 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731440460 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731440460 Building ZINC000731444195 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731444195 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/96 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731444195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731444195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731444195 none CCn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.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'] dock atom type numbers: [5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 18, 18, 18, 18, 18, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 23, 25, 25, 25, 25, 54, 13, 13, 10, 10, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/97 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731444195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731444195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731444195 none CCn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.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'] dock atom type numbers: [5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 21, 21, 21, 21, 21, 15, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 26, 28, 28, 28, 28, 63, 15, 15, 9, 9, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731444195 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 Building ZINC000731444195 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731444195 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 96) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/96: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731444195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731444195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731444195 none CCn1c(S)nnc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.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'] dock atom type numbers: [5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 18, 18, 18, 18, 18, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 23, 25, 25, 25, 25, 54, 13, 13, 10, 10, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 97) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/97: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000731444195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731444195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000731444195 none CCn1c(S)nnc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'S.3', 'N.2', 'N.2', 'C.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.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'] dock atom type numbers: [5, 5, 8, 1, 14, 8, 8, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 21, 21, 21, 21, 21, 15, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 26, 28, 28, 28, 28, 63, 15, 15, 9, 9, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731444195 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444195 Building ZINC000731444229 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731444229 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/98 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1) `ZINC000731444229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731444229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000731444229 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 15, 21, 20, 21, 21, 21, 21, 27, 27, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 10, 10, 15, 15, 63, 27, 27, 27, 27, 27, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 180 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/99 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1) `ZINC000731444229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731444229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000731444229 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 3, 9, 14, 20, 19, 20, 20, 20, 20, 27, 27, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 3, 9, 9, 14, 14, 60, 27, 27, 27, 27, 27, 5] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731444229 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 Building ZINC000731444229 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731444229 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 98) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1) `ZINC000731444229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731444229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000731444229 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 8, 8, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 15, 21, 20, 21, 21, 21, 21, 27, 27, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 3, 10, 10, 15, 15, 63, 27, 27, 27, 27, 27, 6] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 180 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 99) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1) `ZINC000731444229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731444229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000731444229 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCc2nnc(S)n2C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 8, 1, 14, 8, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 3, 9, 14, 20, 19, 20, 20, 20, 20, 27, 27, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 3, 9, 9, 14, 14, 60, 27, 27, 27, 27, 27, 5] 150 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000731444229 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000731444229 Building ZINC000456204709 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456204709 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/100 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO) `ZINC000456204709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456204709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000456204709 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 13, 2, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 30, 30, 30, 30, 30, 30, 42, 50, 30, 30, 30, 30, 30, 3, 3, 3, 3, 30, 30, 30, 30, 30, 42, 42, 50, 50, 150] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 334 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/101 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO) `ZINC000456204709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456204709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000456204709 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 13, 2, 13, 1, 1, 1, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 28, 45, 50, 28, 28, 28, 28, 28, 3, 3, 3, 3, 28, 28, 28, 28, 28, 45, 45, 50, 50, 150] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456204709 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 Building ZINC000456204709 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456204709 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 100) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/100: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO) `ZINC000456204709.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456204709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000456204709 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 30, 30, 13, 2, 17, 1, 1, 1, 3, 3, 1, 3, 3, 3, 30, 30, 30, 30, 30, 30, 42, 50, 30, 30, 30, 30, 30, 3, 3, 3, 3, 30, 30, 30, 30, 30, 42, 42, 50, 50, 150] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 334 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 101) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO) `ZINC000456204709.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456204709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000456204709 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)N1CCO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 10, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 28, 28, 13, 2, 13, 1, 1, 1, 3, 3, 1, 3, 3, 3, 28, 28, 28, 28, 28, 28, 45, 50, 28, 28, 28, 28, 28, 3, 3, 3, 3, 28, 28, 28, 28, 28, 45, 45, 50, 50, 150] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456204709 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456204709 Building ZINC000553741341 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553741341 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/102 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553741341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741341 none CS(=O)(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/103 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553741341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741341 none CS(=O)(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 20, 20, 20, 11, 11, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8] 20 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553741341 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 Building ZINC000553741341 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553741341 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 102) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553741341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741341 none CS(=O)(=O)C[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 103) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/103: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553741341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741341 none CS(=O)(=O)C[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 20, 20, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 20, 20, 20, 11, 11, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8] 20 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553741341 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741341 Building ZINC000553741342 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553741342 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/104 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553741342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741342 none CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 22, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 22, 22, 22, 13, 13, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8] 22 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/105 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553741342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741342 none CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553741342 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 Building ZINC000553741342 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000553741342 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 104) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000553741342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741342 none CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 22, 22, 8, 8, 8, 8, 8, 2, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 22, 22, 22, 13, 13, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8] 22 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 105) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000553741342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000553741342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000553741342 none CS(=O)(=O)C[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000553741342 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000553741342 Building ZINC000179217338 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179217338 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/106 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/107 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 22, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/108 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/108' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 22, 22, 20, 22, 22, 22, 22, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/109 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/109' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 16, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179217338 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 Building ZINC000179217338 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179217338 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 106) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 107) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 22, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 108) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 22, 22, 20, 22, 22, 22, 22, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 109) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 16, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179217338 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 Building ZINC000179217338 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179217338 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 106) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 107) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 22, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 108) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 22, 22, 20, 22, 22, 22, 22, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 109) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 16, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179217338 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 Building ZINC000179217338 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179217338 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 106) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 107) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 22, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 108) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 22, 22, 20, 22, 22, 22, 22, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 109) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1) `ZINC000179217338.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179217338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179217338 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 23, 23, 16, 23, 23, 23, 23, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179217338 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179217338 Building ZINC000456300821 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456300821 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/110 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000456300821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000456300821 none CCS(=O)(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 14, 41, 41, 14, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/111 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000456300821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000456300821 none CCS(=O)(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 14, 42, 42, 14, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456300821 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 Building ZINC000456300821 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456300821 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 110) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/110: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000456300821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000456300821 none CCS(=O)(=O)C1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 14, 41, 41, 14, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 111) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/111: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000456300821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456300821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000456300821 none CCS(=O)(=O)C1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 14, 42, 42, 14, 14, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 49, 49, 49, 49, 49, 14, 14, 14, 3, 3, 3, 3, 14, 14] 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]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456300821 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456300821 Building ZINC000456727932 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727932 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/112 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727932 none O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 14, 14, 14, 14, 81, 14, 14, 5, 8, 8, 5, 8, 8, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/113 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727932 none O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 69, 11, 11, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727932 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 Building ZINC000456727932 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727932 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 112) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727932 none O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 14, 14, 14, 14, 81, 14, 14, 5, 8, 8, 5, 8, 8, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 113) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727932 none O=C(N1CC[C@@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 69, 11, 11, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 170 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727932 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727932 Building ZINC000456727936 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727936 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/114 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727936 none O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 78, 13, 13, 5, 8, 8, 5, 8, 8, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/115 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727936 none O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 4, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 84, 11, 11, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727936 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 Building ZINC000456727936 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727936 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 114) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/114: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727936 none O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 8, 8, 5, 13, 13, 13, 13, 78, 13, 13, 5, 8, 8, 5, 8, 8, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 115) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/115: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727936 none O=C(N1CC[C@@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 4, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 84, 11, 11, 6, 9, 9, 6, 9, 9, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727936 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727936 Building ZINC000456727940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/116 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727940 none O=C(N1CC[C@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 4, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 13, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 13, 13, 13, 13, 87, 13, 13, 6, 7, 7, 6, 7, 7, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/117 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727940 none O=C(N1CC[C@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 6, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 14, 14, 14, 14, 81, 14, 14, 5, 7, 7, 5, 7, 7, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 Building ZINC000456727940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 116) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/116: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727940 none O=C(N1CC[C@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 4, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 13, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 13, 13, 13, 13, 87, 13, 13, 6, 7, 7, 6, 7, 7, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 117) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/117: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727940 none O=C(N1CC[C@H]([C@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 6, 14, 14, 14, 14, 14, 27, 27, 27, 27, 27, 27, 14, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 14, 14, 14, 14, 81, 14, 14, 5, 7, 7, 5, 7, 7, 5] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727940 Building ZINC000456727944 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727944 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/118 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727944 none O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 13, 13, 13, 13, 69, 13, 13, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/119 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727944 none O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 15, 15, 15, 15, 15, 23, 23, 23, 23, 23, 23, 15, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 15, 15, 15, 15, 69, 15, 15, 6, 10, 10, 6, 10, 10, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727944 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 Building ZINC000456727944 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456727944 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 118) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/118: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456727944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727944 none O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 3, 13, 13, 13, 13, 13, 23, 23, 23, 23, 23, 23, 13, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 13, 13, 13, 13, 69, 13, 13, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 155 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 119) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/119: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456727944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456727944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456727944 none O=C(N1CC[C@H]([C@@H](O)C(F)(F)F)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', 'H', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 7, 12, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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, 4, 7, 7, 7, 7, 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] 1 hydrogens 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, 1, 5, 15, 15, 15, 15, 15, 23, 23, 23, 23, 23, 23, 15, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 15, 15, 15, 15, 69, 15, 15, 6, 10, 10, 6, 10, 10, 6] 150 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456727944 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456727944 Building ZINC000456728988 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456728988 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/120 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456728988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728988 none O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 10, 10, 10, 14, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/121 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456728988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728988 none O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 9, 9, 9, 13, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456728988 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 Building ZINC000456728988 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456728988 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 120) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728988.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456728988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728988 none O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 10, 10, 10, 14, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 121) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728988.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456728988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728988 none O=C(N1CCN([C@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 9, 9, 9, 13, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 1, 1, 1, 5, 5, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456728988 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728988 Building ZINC000456728990 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456728990 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/122 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456728990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728990 none O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 8, 8, 8, 12, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/123 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456728990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728990 none O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 10, 10, 10, 14, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456728990 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 Building ZINC000456728990 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456728990 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 122) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/122: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456728990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728990 none O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 8, 8, 8, 12, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 8, 8, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 8, 8, 8, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 93 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 123) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/123: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000456728990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456728990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000456728990 none O=C(N1CCN([C@@H]2CCNC(=O)CC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 10, 10, 10, 14, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 1, 1, 1, 4, 4, 7, 7, 4, 7, 7, 7, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 4, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456728990 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456728990 Building ZINC000456737961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/124 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/125 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/126 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/126' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/127 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/127' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 Building ZINC000456737961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 124) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 125) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 126) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 127) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 Building ZINC000456737961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 124) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 125) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 126) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 127) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 Building ZINC000456737961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 124) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/124: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 125) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/125: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 126) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/126: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 8, 14, 21, 21, 21, 21, 37, 37, 37, 37, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 37, 37, 21, 21, 21, 21, 21, 21, 21] 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: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 127) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/127: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@H](C)C1) `ZINC000456737961.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737961 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 14, 21, 21, 21, 21, 36, 36, 36, 36, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 36, 21, 21, 21, 21, 21, 21, 21] 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: 122 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737961 Building ZINC000456737965 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737965 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/128 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/129 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/130 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/130' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/131 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/131' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737965 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 Building ZINC000456737965 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737965 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 128) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 129) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 130) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 131) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737965 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 Building ZINC000456737965 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737965 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 128) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 129) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 130) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 131) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737965 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 Building ZINC000456737965 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000456737965 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 128) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/128: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 129) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/129: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 130) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 18, 21, 21, 21, 21, 38, 38, 38, 38, 21, 21, 21, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 38, 38, 21, 21, 21, 21, 21, 21, 21] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 131) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[C@@H](C)C1) `ZINC000456737965.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000456737965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456737965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CC(F)(F)F)C[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', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 15, 15, 15, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 9, 15, 23, 23, 23, 23, 39, 39, 39, 39, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 39, 39, 23, 23, 23, 23, 23, 23, 23] 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: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456737965 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456737965 Building ZINC000456763721 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456763721 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/132 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1) `ZINC000456763721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456763721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763721 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 22, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/133 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1) `ZINC000456763721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456763721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763721 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 24, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456763721 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 Building ZINC000456763721 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456763721 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 132) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/132: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1) `ZINC000456763721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456763721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763721 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 22, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 133) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/133: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1) `ZINC000456763721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456763721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763721 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 24, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 116 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456763721 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763721 Building ZINC000456763722 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456763722 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/134 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1) `ZINC000456763722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456763722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763722 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 21, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13] 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: 118 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/135 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1) `ZINC000456763722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456763722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763722 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 24, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13] 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: 122 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456763722 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 Building ZINC000456763722 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456763722 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 134) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1) `ZINC000456763722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456763722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763722 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 21, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 13, 13, 13] 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: 118 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 135) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1) `ZINC000456763722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456763722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000456763722 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H]2CCNC(=O)CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 5, 8, 1, 11, 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] 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 24, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 13, 13, 13, 13] 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: 122 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456763722 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456763722 Building ZINC000456797509 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797509 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/136 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797509 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 14, 14, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 14, 14, 14, 14, 14, 9] 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, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/137 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797509 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 17, 17, 11, 17, 17, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 17, 17, 11, 17, 17, 10] 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, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797509 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 Building ZINC000456797509 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797509 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 136) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797509.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797509 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 14, 14, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 14, 14, 14, 14, 14, 9] 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, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 137) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/137: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797509.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797509 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 17, 17, 11, 17, 17, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 17, 17, 11, 17, 17, 10] 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, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797509 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797509 Building ZINC000456797516 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797516 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/138 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797516 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 14, 14, 9, 14, 14, 9] 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, 43, 44]) total number of confs: 63 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/139 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797516 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 20, 20, 10, 20, 20, 10] 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, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797516 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 Building ZINC000456797516 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797516 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 138) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/138: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797516 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 3, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 9, 9, 14, 14, 9, 14, 14, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 14, 14, 9, 14, 14, 9] 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, 43, 44]) total number of confs: 63 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 139) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/139: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797516 none O=C(N1CCS(=O)(=O)[C@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 10, 10, 20, 20, 10, 20, 20, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 10, 20, 20, 10, 20, 20, 10] 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, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797516 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797516 Building ZINC000456797518 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797518 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/140 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797518 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 20, 20, 12, 20, 20, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 20, 20, 12, 20, 20, 10] 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, 43, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/141 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797518 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 16, 16, 11, 16, 16, 11] 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, 43, 44]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797518 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 Building ZINC000456797518 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797518 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 140) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/140: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797518 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 10, 10, 10, 10, 20, 20, 12, 20, 20, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 10, 20, 20, 12, 20, 20, 10] 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, 43, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 141) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/141: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797518 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 16, 16, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 16, 16, 11, 16, 16, 11] 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, 43, 44]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797518 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797518 Building ZINC000456797521 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797521 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/142 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797521 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 17, 17, 11, 17, 17, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 17, 17, 11, 17, 17, 10] 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, 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/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/143 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797521 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 13, 13, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 13, 13, 13, 13, 13, 9] 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, 43, 44]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797521 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 Building ZINC000456797521 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456797521 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 142) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/142: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456797521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797521 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 10, 10, 10, 10, 17, 17, 11, 17, 17, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 17, 17, 11, 17, 17, 10] 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, 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/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 143) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/143: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000456797521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456797521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000456797521 none O=C(N1CCS(=O)(=O)[C@@H]2CCC[C@@H]21)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 9, 9, 9, 13, 13, 13, 13, 13, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 13, 13, 13, 13, 13, 9] 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, 43, 44]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456797521 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456797521 Building ZINC000456800374 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800374 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/144 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800374 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 3, 12, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/145 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800374 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 3, 12, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800374 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 Building ZINC000456800374 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800374 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 144) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800374 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 2, 6, 6, 1, 1, 1, 3, 12, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 11, 11, 11, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 145) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800374 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 2, 6, 6, 1, 1, 1, 3, 12, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 12, 12, 12, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800374 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800374 Building ZINC000456800393 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800393 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/146 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800393 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 3, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/147 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800393 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 3, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800393 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 Building ZINC000456800393 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800393 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 146) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800393 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 3, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 147) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)cc1Cl) `ZINC000456800393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800393 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 3, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800393 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800393 Building ZINC000456800398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/148 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)cc1Cl) `ZINC000456800398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800398 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 3, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/149 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)cc1Cl) `ZINC000456800398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800398 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 Building ZINC000456800398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 148) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)cc1Cl) `ZINC000456800398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800398 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 3, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 16, 16, 16, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 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]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 149) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/149: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)cc1Cl) `ZINC000456800398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800398 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 2, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 13, 13, 13, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800398 Building ZINC000456800404 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800404 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/150 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)cc1Cl) `ZINC000456800404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800404 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 4, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/151 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)cc1Cl) `ZINC000456800404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800404 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 4, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800404 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 Building ZINC000456800404 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456800404 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 150) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)cc1Cl) `ZINC000456800404.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456800404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800404 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 4, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 6, 6, 14, 14, 14, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 151) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)cc1Cl) `ZINC000456800404.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456800404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000456800404 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)[C@@H]3CCC[C@H]32)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 7, 5, 5, 5, 5, 7, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 8, 8, 1, 1, 1, 4, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8] 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]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456800404 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456800404 Building ZINC000456976874 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456976874 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/152 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1) `ZINC000456976874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456976874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000456976874 none COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 8, 8, 8, 8, 6, 2, 8, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 8, 8, 22, 22, 33, 33, 33, 22, 22, 8, 8, 8, 8, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 8, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/153 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1) `ZINC000456976874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456976874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000456976874 none COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 9, 9, 9, 9, 6, 2, 8, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 2, 9, 9, 23, 23, 35, 35, 35, 23, 23, 9, 9, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456976874 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 Building ZINC000456976874 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000456976874 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 152) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/152: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1) `ZINC000456976874.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000456976874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000456976874 none COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 22, 22, 22, 8, 8, 8, 8, 6, 2, 8, 1, 1, 1, 3, 3, 3, 3, 7, 7, 7, 3, 8, 8, 22, 22, 33, 33, 33, 22, 22, 8, 8, 8, 8, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 8, 8, 8, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 153) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/153: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1) `ZINC000456976874.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000456976874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000456976874 none COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 9, 9, 9, 9, 6, 2, 8, 1, 1, 1, 2, 2, 2, 2, 6, 6, 6, 2, 9, 9, 23, 23, 35, 35, 35, 23, 23, 9, 9, 9, 9, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 9, 9, 9, 9, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 86 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000456976874 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000456976874 Building ZINC000457022838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457022838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/154 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)nc1) `ZINC000457022838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457022838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000457022838 none COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 16, 16, 16, 16, 7, 2, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 16, 39, 39, 49, 49, 49, 39, 39, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 39] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/155 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)nc1) `ZINC000457022838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457022838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000457022838 none COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 7, 2, 10, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 17, 17, 39, 39, 50, 50, 50, 39, 39, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 39] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457022838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 Building ZINC000457022838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457022838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 154) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/154: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)nc1) `ZINC000457022838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457022838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000457022838 none COc1ccc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 39, 39, 16, 16, 16, 16, 7, 2, 10, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 16, 39, 39, 49, 49, 49, 39, 39, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 39] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 94 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 155) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/155: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)nc1) `ZINC000457022838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457022838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000457022838 none COc1ccc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 17, 17, 7, 2, 10, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 17, 17, 39, 39, 50, 50, 50, 39, 39, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 39] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457022838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457022838 Building ZINC000554454893 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554454893 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/156 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1) `ZINC000554454893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554454893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000554454893 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1 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', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 7, 8, 8, 8, 8, 24, 24, 24, 46, 46, 46, 46, 46, 46, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 24, 46, 46, 46, 46, 46, 46, 46, 8, 8, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/157 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1) `ZINC000554454893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554454893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000554454893 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1 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', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 7, 8, 8, 8, 8, 25, 25, 25, 49, 49, 49, 49, 49, 49, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 25, 49, 49, 49, 49, 49, 49, 49, 8, 8, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000554454893 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 Building ZINC000554454893 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554454893 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 156) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1) `ZINC000554454893.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554454893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000554454893 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1 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', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 7, 8, 8, 8, 8, 24, 24, 24, 46, 46, 46, 46, 46, 46, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 24, 46, 46, 46, 46, 46, 46, 46, 8, 8, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 157) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1) `ZINC000554454893.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554454893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000554454893 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)NCc2ccccc2)CC1 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', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 7, 8, 8, 8, 8, 25, 25, 25, 49, 49, 49, 49, 49, 49, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 25, 49, 49, 49, 49, 49, 49, 49, 8, 8, 8, 8] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 154 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000554454893 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554454893 Building ZINC000457127471 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127471 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/158 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/159 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/160 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/160' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/161 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/161' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127471 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 Building ZINC000457127471 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127471 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 158) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 159) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 160) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 161) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127471 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 Building ZINC000457127471 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127471 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 158) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 159) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 160) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 161) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127471 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 Building ZINC000457127471 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127471 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 158) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 159) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 24, 24, 24, 24, 24, 44, 48, 24, 24, 19, 2, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 24, 24, 24, 24, 24, 44, 44, 48, 48, 144, 24, 24, 24, 24, 3, 3, 3, 3] 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]) total number of confs: 323 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 160) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/160: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 161) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127471.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127471 none C[C@@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 22, 22, 22, 22, 22, 45, 50, 22, 22, 16, 2, 18, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 22, 22, 45, 45, 50, 50, 150, 22, 22, 22, 22, 3, 3, 3, 3] 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]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127471 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127471 Building ZINC000457127473 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127473 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/162 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/163 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/164 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/164' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/165 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/165' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127473 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 Building ZINC000457127473 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127473 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 162) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 163) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 164) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 165) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127473 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 Building ZINC000457127473 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127473 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 162) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 163) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 164) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 165) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127473 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 Building ZINC000457127473 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457127473 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 162) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 163) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/163: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 150 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]) total number of confs: 292 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 164) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/164: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 165) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/165: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457127473.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457127473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000457127473 none C[C@H]1CN(CCO)CCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 9, 9, 35, 41, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 35, 35, 41, 41, 123, 9, 9, 9, 9, 6, 6, 6, 6] 129 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]) total number of confs: 281 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457127473 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457127473 Building ZINC000457134929 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457134929 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/166 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1) `ZINC000457134929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457134929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000457134929 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 2, 4, 2, 2, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/167 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1) `ZINC000457134929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457134929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000457134929 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 2, 4, 2, 2, 13, 13, 13, 13, 50, 50] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457134929 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 Building ZINC000457134929 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457134929 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 166) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1) `ZINC000457134929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457134929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000457134929 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 8, 1, 8, 1, 1, 1, 2, 2, 1, 1, 2, 2, 12, 12, 12, 12, 32, 32, 50, 50, 50, 50, 12, 12, 12, 12, 12, 2, 2, 4, 2, 2, 12, 12, 12, 12, 50, 50] 100 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 167) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1) `ZINC000457134929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457134929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000457134929 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCN1C(=O)c1cscn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 9, 2, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 13, 13, 13, 13, 33, 33, 50, 50, 50, 50, 13, 13, 13, 13, 13, 2, 2, 4, 2, 2, 13, 13, 13, 13, 50, 50] 100 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457134929 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457134929 Building ZINC000457140787 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140787 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/168 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/169 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/170 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/170' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/171 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/171' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140787 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 Building ZINC000457140787 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140787 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 168) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 169) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 170) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 171) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140787 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 Building ZINC000457140787 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140787 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 168) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 169) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 170) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 171) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140787 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 Building ZINC000457140787 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140787 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 168) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 169) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 170) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 7, 7, 7, 7, 18, 24, 7, 7, 7, 7, 4, 4, 4, 13, 13, 5, 13, 13, 4, 4, 4, 7, 7, 7, 7, 18, 18, 24, 24, 72, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 171) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@@H]1C) `ZINC000457140787.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140787 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 16, 16, 4, 4, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 23, 33, 7, 7, 7, 7, 4, 4, 4, 16, 16, 4, 16, 16, 4, 4, 4, 7, 7, 7, 7, 23, 23, 33, 33, 99, 7, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 280 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140787 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140787 Building ZINC000457140792 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140792 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/172 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/172' -> `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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/173 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/173' -> `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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/174 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/174' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/175 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/175' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140792 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 Building ZINC000457140792 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140792 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 172) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 173) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 174) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 175) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140792 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 Building ZINC000457140792 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140792 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 172) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 173) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 174) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 175) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140792 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 Building ZINC000457140792 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000457140792 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 172) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 173) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 174) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 8, 12, 12, 4, 4, 1, 1, 1, 2, 9, 13, 14, 14, 14, 14, 30, 37, 14, 14, 14, 14, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 14, 14, 14, 14, 30, 30, 37, 37, 111, 14, 14, 14, 14, 14] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 297 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 175) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)N1CCN(CCO)C[C@H]1C) `ZINC000457140792.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000457140792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000457140792 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCN(CCO)C[C@H]1C NO_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', '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', '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, 12, 5, 5, 7, 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] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 4, 11, 11, 4, 4, 1, 1, 1, 2, 11, 15, 16, 16, 16, 16, 33, 41, 16, 16, 16, 16, 4, 4, 4, 11, 11, 6, 11, 11, 4, 4, 4, 16, 16, 16, 16, 33, 33, 41, 41, 123, 16, 16, 16, 16, 16] 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, 47, 48, 49, 50, 51, 52]) total number of confs: 314 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457140792 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457140792 Building ZINC000457130562 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457130562 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/176 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1) `ZINC000457130562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457130562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000457130562 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 25, 25, 48, 48, 48, 48, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 48, 48, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/177 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1) `ZINC000457130562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457130562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000457130562 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 31, 31, 48, 48, 48, 48, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 48, 48, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457130562 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 Building ZINC000457130562 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457130562 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 176) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1) `ZINC000457130562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457130562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000457130562 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 25, 25, 48, 48, 48, 48, 10, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 48, 48, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 177) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1) `ZINC000457130562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457130562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000457130562 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cscn2)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 31, 31, 48, 48, 48, 48, 13, 13, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 48, 48, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457130562 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457130562 Building ZINC000554509462 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554509462 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/178 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1) `ZINC000554509462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554509462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000554509462 none COCC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 22, 22, 22, 22, 22, 50, 50, 50, 48, 48, 6, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/179 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1) `ZINC000554509462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554509462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000554509462 none COCC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 50, 50, 50, 48, 48, 6, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000554509462 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 Building ZINC000554509462 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000554509462 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 178) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/178: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1) `ZINC000554509462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000554509462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000554509462 none COCC1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 22, 22, 22, 22, 22, 50, 50, 50, 48, 48, 6, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 179) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/179: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1) `ZINC000554509462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000554509462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000554509462 none COCC1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 22, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 22, 22, 22, 22, 22, 50, 50, 50, 48, 48, 6, 4, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000554509462 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000554509462 Building ZINC000457250248 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457250248 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/180 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C) `ZINC000457250248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457250248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000457250248 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 29, 29, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 49, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/181 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C) `ZINC000457250248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457250248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000457250248 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 2, 8, 8, 9, 9, 9, 9, 24, 24, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 49, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457250248 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 Building ZINC000457250248 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457250248 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 180) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C) `ZINC000457250248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457250248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000457250248 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 29, 29, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 49, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 181) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C) `ZINC000457250248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457250248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000457250248 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C(=O)c2cc(C)[nH]n2)C[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'H', 'N.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 5, 8, 6, 8, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 2, 8, 8, 9, 9, 9, 9, 24, 24, 49, 49, 49, 49, 49, 49, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 49, 49, 49, 49, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457250248 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457250248 Building ZINC000457253563 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253563 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/182 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253563 none O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 16, 44, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/183 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253563 none O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 15, 44, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 6, 6, 6, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253563 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 Building ZINC000457253563 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253563 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 182) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253563.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253563 none O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 16, 44, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 1, 5, 5, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 183) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253563.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253563 none O=C(N[C@@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 15, 44, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 6, 6, 1, 6, 6, 6, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253563 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253563 Building ZINC000457253564 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253564 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/184 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253564 none O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/185 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253564 none O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 45, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253564 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 Building ZINC000457253564 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253564 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 184) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253564.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253564 none O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 1, 6, 6, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 185) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253564.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253564 none O=C(N[C@H]1C[C@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 45, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1, 5, 5, 1, 1, 5, 5, 7, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253564 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253564 Building ZINC000457253566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/186 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253566 none O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 4, 6, 6, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/187 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253566 none O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 6, 6, 6, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 Building ZINC000457253566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 186) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253566 none O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 4, 6, 6, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 187) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253566 none O=C(N[C@@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 6, 6, 1, 6, 6, 6, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253566 Building ZINC000457253569 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253569 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/188 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253569 none O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/189 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253569 none O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253569 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 Building ZINC000457253569 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457253569 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 188) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/188: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253569.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457253569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253569 none O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 189) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/189: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000457253569.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457253569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000457253569 none O=C(N[C@H]1C[C@@H]2CCCCN2C1=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 9, 15, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 6, 6, 1, 1, 6, 6, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6] 50 rigid atoms, others: [1, 15, 16, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457253569 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457253569 Building ZINC000457266498 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457266498 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/190 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1) `ZINC000457266498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457266498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000457266498 none Cc1cc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 8, 31, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/191 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1) `ZINC000457266498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457266498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000457266498 none Cc1cc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 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, 11, 33, 11, 11, 11, 9, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457266498 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 Building ZINC000457266498 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457266498 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 190) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1) `ZINC000457266498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457266498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000457266498 none Cc1cc(C(=O)N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 31, 8, 31, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 191) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1) `ZINC000457266498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457266498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000457266498 none Cc1cc(C(=O)N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)[C@H](C)C2)n[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 5, 5, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 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] 0 hydrogens need rotated 50 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, 11, 33, 11, 11, 11, 9, 2, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457266498 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457266498 Building ZINC000457258254 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457258254 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/192 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457258254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258254 none CC[C@@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 4, 10, 26, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 28, 28, 28, 17, 17, 17, 17, 17, 26, 26, 27, 27, 27, 4, 3, 3, 3, 3, 28, 28, 28] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/193 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457258254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258254 none CC[C@@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 25, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 18, 18, 18, 18, 18, 25, 25, 28, 28, 28, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457258254 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 Building ZINC000457258254 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457258254 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 192) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457258254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258254 none CC[C@@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 4, 10, 26, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 28, 28, 28, 17, 17, 17, 17, 17, 26, 26, 27, 27, 27, 4, 3, 3, 3, 3, 28, 28, 28] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 193) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457258254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258254 none CC[C@@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 25, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 18, 18, 18, 18, 18, 25, 25, 28, 28, 28, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457258254 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258254 Building ZINC000457258255 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457258255 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/194 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457258255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258255 none CC[C@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 25, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 18, 18, 18, 18, 18, 25, 25, 28, 28, 28, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/195 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457258255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258255 none CC[C@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 4, 10, 26, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 10, 27, 27, 27, 17, 17, 17, 17, 17, 26, 26, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457258255 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 Building ZINC000457258255 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457258255 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 194) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/194: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457258255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258255 none CC[C@](COC)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 11, 25, 28, 5, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 18, 18, 18, 18, 18, 25, 25, 28, 28, 28, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 195) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/195: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000457258255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457258255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 43 natoms 42 natoms 41 natoms 40 names: ZINC000457258255 none CC[C@](COC)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 4, 10, 26, 27, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 10, 27, 27, 27, 17, 17, 17, 17, 17, 26, 26, 27, 27, 27, 4, 3, 3, 3, 3, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457258255 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457258255 Building ZINC000457357848 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457357848 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/196 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000457357848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457357848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000457357848 none COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 24, 24, 19, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/197 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000457357848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457357848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000457357848 none COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 24, 18, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457357848 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 Building ZINC000457357848 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457357848 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 196) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000457357848.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457357848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000457357848 none COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 24, 24, 19, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 197) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000457357848.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457357848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000457357848 none COc1ccccc1[C@H]1[C@@H](N)CCCN1C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 7, 5, 7, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 24, 18, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 82 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457357848 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457357848 Building ZINC001746514940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001746514940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/198 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1) `ZINC001746514940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001746514940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001746514940 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/199 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1) `ZINC001746514940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001746514940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001746514940 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001746514940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 Building ZINC001746514940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001746514940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 198) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/198: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1) `ZINC001746514940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001746514940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001746514940 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 28, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 199) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/199: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1) `ZINC001746514940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001746514940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001746514940 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@@H]2C[C@H]3CC[C@@H]2O3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 26, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001746514940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001746514940 Building ZINC000555081813 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555081813 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/200 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000555081813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555081813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000555081813 none COc1ncccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 25, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 31, 31, 31, 31, 31, 31, 25, 25, 14, 14, 3, 6, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/201 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000555081813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555081813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000555081813 none COc1ncccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 26, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 32, 32, 32, 32, 32, 32, 26, 26, 14, 14, 3, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000555081813 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 Building ZINC000555081813 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555081813 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 200) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/200: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000555081813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555081813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000555081813 none COc1ncccc1CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 25, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 31, 31, 31, 31, 31, 31, 25, 25, 14, 14, 3, 6, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 201) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/201: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ncccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000555081813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555081813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000555081813 none COc1ncccc1CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 26, 14, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 32, 32, 32, 32, 32, 32, 26, 26, 14, 14, 3, 6, 7, 7, 6, 7, 7, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000555081813 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555081813 Building ZINC000457880828 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457880828 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/202 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/202' -> `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)NCCc1cn(C)cn1) `ZINC000457880828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457880828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000457880828 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 32, 39, 39, 39, 39, 39, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 3, 17, 17, 32, 32, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/203 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/203' -> `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)NCCc1cn(C)cn1) `ZINC000457880828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457880828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000457880828 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 31, 38, 38, 38, 38, 38, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 3, 17, 17, 31, 31, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457880828 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 Building ZINC000457880828 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457880828 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 202) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1) `ZINC000457880828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457880828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000457880828 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 32, 39, 39, 39, 39, 39, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 3, 17, 17, 32, 32, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 203) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1) `ZINC000457880828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457880828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000457880828 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cn(C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 3, 3, 3, 17, 31, 38, 38, 38, 38, 38, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 3, 17, 17, 31, 31, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457880828 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457880828 Building ZINC000457907970 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457907970 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/204 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1) `ZINC000457907970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457907970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907970 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 25, 17, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 17, 17, 17, 17, 17, 17, 51, 25, 25, 75, 17, 17] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 233 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/205 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1) `ZINC000457907970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457907970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907970 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 2, 13, 15, 20, 20, 20, 20, 20, 20, 38, 20, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 20, 20, 20, 20, 20, 20, 60, 38, 38, 114, 20, 20] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 321 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457907970 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 Building ZINC000457907970 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457907970 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 204) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1) `ZINC000457907970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457907970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907970 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 25, 17, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 17, 17, 17, 17, 17, 17, 51, 25, 25, 75, 17, 17] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 233 number of broken/clashed sets: 177 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 205) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1) `ZINC000457907970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457907970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907970 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 6, 10, 10, 3, 3, 1, 1, 1, 2, 13, 15, 20, 20, 20, 20, 20, 20, 38, 20, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 20, 20, 20, 20, 20, 20, 60, 38, 38, 114, 20, 20] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 321 number of broken/clashed sets: 129 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457907970 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907970 Building ZINC000457907971 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457907971 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/206 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1) `ZINC000457907971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457907971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907971 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 13, 17, 22, 22, 22, 22, 22, 22, 33, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 66, 33, 33, 99, 22, 22] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/207 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1) `ZINC000457907971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457907971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907971 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 5, 11, 11, 3, 3, 1, 1, 1, 2, 13, 14, 19, 19, 19, 19, 19, 19, 22, 19, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 19, 19, 19, 19, 19, 19, 57, 22, 22, 66, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 213 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457907971 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 Building ZINC000457907971 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457907971 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 206) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1) `ZINC000457907971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457907971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907971 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 13, 17, 22, 22, 22, 22, 22, 22, 33, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 66, 33, 33, 99, 22, 22] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 292 number of broken/clashed sets: 144 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 207) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1) `ZINC000457907971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457907971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000457907971 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@](O)(CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 11, 11, 5, 11, 11, 3, 3, 1, 1, 1, 2, 13, 14, 19, 19, 19, 19, 19, 19, 22, 19, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 19, 19, 19, 19, 19, 19, 57, 22, 22, 66, 19, 19] 450 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 208 number of broken/clashed sets: 213 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457907971 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457907971 Building ZINC000555159582 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555159582 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/208 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1) `ZINC000555159582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555159582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000555159582 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 14, 14, 14, 20, 20, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 8] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/209 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1) `ZINC000555159582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555159582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000555159582 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 9, 11, 15, 15, 15, 15, 15, 31, 31, 31, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000555159582 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 Building ZINC000555159582 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000555159582 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 208) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/208: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1) `ZINC000555159582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000555159582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000555159582 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 14, 14, 14, 20, 20, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 20, 8, 8, 8, 8] 22 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 209) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1) `ZINC000555159582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000555159582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000555159582 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1CCCN(S(=O)(=O)C2CC2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 14, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 9, 11, 15, 15, 15, 15, 15, 31, 31, 31, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 15, 15, 45, 45, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000555159582 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000555159582 Building ZINC000457974244 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457974244 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/210 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCOCC2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000457974244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457974244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000457974244 none O=C(NCC1(N2CCOCC2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 28, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/211 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCOCC2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000457974244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457974244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000457974244 none O=C(NCC1(N2CCOCC2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 29, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457974244 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 Building ZINC000457974244 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457974244 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 210) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCOCC2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000457974244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457974244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000457974244 none O=C(NCC1(N2CCOCC2)CCOCC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 28, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 211) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/211: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCOCC2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000457974244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457974244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000457974244 none O=C(NCC1(N2CCOCC2)CCOCC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 29, 49, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 160 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000457974244 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000457974244 Building ZINC000458041987 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458041987 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/212 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/212' -> `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]1c2sccc2OC(C)(C)[C@@H]1O) `ZINC000458041987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458041987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000458041987 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 14, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 27, 27, 27, 27, 81] 99 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/213 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/213' -> `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]1c2sccc2OC(C)(C)[C@@H]1O) `ZINC000458041987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458041987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000458041987 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 14, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 30, 90] 111 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458041987 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 Building ZINC000458041987 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458041987 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 212) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/212: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O) `ZINC000458041987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458041987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000458041987 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 14, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 27, 27, 27, 27, 81] 99 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 213) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/213: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O) `ZINC000458041987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458041987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000458041987 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1c2sccc2OC(C)(C)[C@@H]1O 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.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 1, 14, 1, 1, 1, 12, 5, 5, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 9, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 30, 30, 30, 30, 30, 30, 30, 30, 90] 111 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458041987 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458041987 Building ZINC000179354881 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179354881 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/214 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1) `ZINC000179354881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179354881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179354881 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 8, 8, 8, 25, 25, 25, 25, 25, 25, 5, 5, 3, 3, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/215 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1) `ZINC000179354881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179354881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179354881 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 27, 27, 27, 27, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179354881 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 Building ZINC000179354881 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179354881 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 214) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/214: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1) `ZINC000179354881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179354881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179354881 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 3, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 8, 8, 8, 25, 25, 25, 25, 25, 25, 5, 5, 3, 3, 11, 11, 11, 11, 11, 3, 5, 5, 5, 5, 5, 8, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 3] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 215) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/215: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1) `ZINC000179354881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179354881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179354881 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)NCc3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 8, 8, 8, 27, 27, 27, 27, 27, 27, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 8, 27, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179354881 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179354881 Building ZINC000458160891 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458160891 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/216 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C) `ZINC000458160891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458160891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160891 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 11, 30, 30, 30, 30, 30, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 26, 26, 78, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/217 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C) `ZINC000458160891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458160891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160891 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 7, 20, 20, 20, 20, 20, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 22, 22, 66, 20, 20, 20, 20, 20] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458160891 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 Building ZINC000458160891 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458160891 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 216) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C) `ZINC000458160891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458160891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160891 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 11, 30, 30, 30, 30, 30, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 26, 26, 78, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 231 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 217) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C) `ZINC000458160891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458160891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160891 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 7, 20, 20, 20, 20, 20, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 4, 4, 22, 22, 66, 20, 20, 20, 20, 20] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 186 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458160891 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160891 Building ZINC000458160903 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458160903 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/218 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C) `ZINC000458160903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458160903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160903 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 7, 20, 20, 20, 20, 20, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 22, 22, 66, 20, 20, 20, 20, 20] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/219 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C) `ZINC000458160903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458160903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160903 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 23, 8, 25, 25, 25, 25, 25, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 6, 23, 23, 69, 25, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458160903 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 Building ZINC000458160903 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458160903 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 218) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/218: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C) `ZINC000458160903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458160903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160903 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 4, 4, 4, 7, 7, 22, 7, 20, 20, 20, 20, 20, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 4, 22, 22, 66, 20, 20, 20, 20, 20] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 219) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/219: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C) `ZINC000458160903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458160903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000458160903 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)c1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 23, 8, 25, 25, 25, 25, 25, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 6, 23, 23, 69, 25, 25, 25, 25, 25] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458160903 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458160903 Building ZINC000776372441 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776372441 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/220 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000776372441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776372441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000776372441 none CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 5, 5, 27, 27, 27, 1, 3, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 27, 27, 27, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/221 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000776372441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776372441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000776372441 none CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 4, 5, 7, 7, 24, 24, 24, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 24, 24, 24, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776372441 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 Building ZINC000776372441 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776372441 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 220) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/220: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000776372441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776372441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000776372441 none CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 4, 5, 5, 27, 27, 27, 1, 3, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 5, 27, 27, 27, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 171 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 221) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/221: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000776372441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776372441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000776372441 none CC(C)(C)N(CCS(C)(=O)=O)C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 14, 5, 11, 11, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 9, 4, 5, 7, 7, 24, 24, 24, 1, 4, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7, 24, 24, 24, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776372441 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776372441 Building ZINC000179381770 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179381770 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/222 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1) `ZINC000179381770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179381770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179381770 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 17, 17, 18, 18, 17, 18, 18, 9, 9, 6, 6, 14, 14, 14, 14, 14, 6, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/223 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1) `ZINC000179381770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179381770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179381770 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 8, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179381770 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 Building ZINC000179381770 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179381770 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 222) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/222: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1) `ZINC000179381770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179381770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179381770 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 17, 17, 18, 18, 17, 18, 18, 9, 9, 6, 6, 14, 14, 14, 14, 14, 6, 2, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 223) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/223: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1) `ZINC000179381770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179381770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179381770 none CCn1cc([C@]([O-])([SiH3])C(=O)NC2CCN(C(=O)c3ccccc3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 8, 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, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 8, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179381770 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179381770 Building ZINC001445076106 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445076106 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/224 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O) `ZINC001445076106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445076106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001445076106 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 21, 34, 21, 21, 21, 21, 6, 21, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/225 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O) `ZINC001445076106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445076106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001445076106 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 21, 21, 21, 21, 6, 21, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 21, 21, 35, 35, 35, 35, 35, 35, 35, 21, 21, 6, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001445076106 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 Building ZINC001445076106 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001445076106 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 224) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/224: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O) `ZINC001445076106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001445076106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001445076106 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 21, 34, 21, 21, 21, 21, 6, 21, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 21, 21, 34, 34, 34, 34, 34, 34, 34, 21, 21, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 225) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/225: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O) `ZINC001445076106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001445076106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001445076106 none CC(C)N1C(=O)C[C@@H](NC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 21, 21, 21, 21, 6, 21, 6, 1, 6, 1, 1, 1, 6, 6, 6, 1, 6, 6, 6, 21, 21, 35, 35, 35, 35, 35, 35, 35, 21, 21, 6, 6, 1, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001445076106 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001445076106 Building ZINC000458346872 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458346872 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/226 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1) `ZINC000458346872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458346872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000458346872 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 18, 18, 12, 18, 18, 18, 29, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 18, 18, 18, 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]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/227 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1) `ZINC000458346872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458346872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000458346872 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 17, 17, 12, 17, 17, 17, 29, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 17, 17, 17, 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]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458346872 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 Building ZINC000458346872 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000458346872 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 226) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1) `ZINC000458346872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000458346872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000458346872 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 18, 18, 12, 18, 18, 18, 29, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 18, 18, 18, 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]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 227) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1) `ZINC000458346872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000458346872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000458346872 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(F)cc1N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 17, 17, 12, 17, 17, 17, 29, 41, 41, 41, 41, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 17, 17, 17, 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]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000458346872 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000458346872 Building ZINC000466274187 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466274187 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/228 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1) `ZINC000466274187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466274187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000466274187 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 13, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 4, 11, 11, 11, 24, 24, 24, 24, 24, 4, 4, 5, 6, 6, 5, 6, 6, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/229 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1) `ZINC000466274187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466274187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000466274187 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 12, 4, 12, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 4, 10, 10, 10, 24, 24, 24, 24, 24, 4, 4, 5, 6, 6, 5, 6, 6, 5, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466274187 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 Building ZINC000466274187 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466274187 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 228) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/228: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1) `ZINC000466274187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466274187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000466274187 none CCOC(=O)CN(C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 4, 13, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 4, 11, 11, 11, 24, 24, 24, 24, 24, 4, 4, 5, 6, 6, 5, 6, 6, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 229) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/229: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1) `ZINC000466274187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466274187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000466274187 none CCOC(=O)CN(C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 12, 4, 12, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 5, 6, 6, 5, 4, 10, 10, 10, 24, 24, 24, 24, 24, 4, 4, 5, 6, 6, 5, 6, 6, 5, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466274187 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466274187 Building ZINC000927946491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927946491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/230 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/230' -> `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(C)(C)C)c1)Cc1ccccc1) `ZINC000927946491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927946491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946491 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 17, 18, 10, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 17, 29, 29, 29, 29, 29, 29, 18, 18, 18, 10, 10, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/231 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/231' -> `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(C)(C)C)c1)Cc1ccccc1) `ZINC000927946491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927946491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946491 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 22, 25, 12, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 30, 30, 30, 30, 30, 30, 25, 25, 25, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927946491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 Building ZINC000927946491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927946491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 230) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/230: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1) `ZINC000927946491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927946491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946491 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 17, 18, 10, 17, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 17, 29, 29, 29, 29, 29, 29, 18, 18, 18, 10, 10, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 231) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/231: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1) `ZINC000927946491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927946491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946491 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 22, 25, 12, 22, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 22, 30, 30, 30, 30, 30, 30, 25, 25, 25, 12, 12, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927946491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946491 Building ZINC000927946492 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927946492 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/232 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/232' -> `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(C)(C)C)c1)Cc1ccccc1) `ZINC000927946492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927946492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946492 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 23, 26, 13, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/233 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/233' -> `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(C)(C)C)c1)Cc1ccccc1) `ZINC000927946492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927946492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946492 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 11, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 18, 29, 29, 29, 29, 29, 29, 19, 19, 19, 11, 11, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927946492 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 Building ZINC000927946492 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927946492 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 232) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/232: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1) `ZINC000927946492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927946492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946492 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 23, 26, 13, 23, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 23, 29, 29, 29, 29, 29, 29, 26, 26, 26, 13, 13, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 233) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/233: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1) `ZINC000927946492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927946492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927946492 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)Cc1ccccc1 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.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 19, 11, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 18, 29, 29, 29, 29, 29, 29, 19, 19, 19, 11, 11, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927946492 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927946492 Building ZINC000330404262 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330404262 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/234 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/234' -> `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(C(=O)N[C@H](C)C(C)C)CC1) `ZINC000330404262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330404262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404262 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 10, 12, 12, 12, 12, 24, 24, 24, 37, 37, 37, 37, 37, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/235 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/235' -> `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(C(=O)N[C@H](C)C(C)C)CC1) `ZINC000330404262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330404262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404262 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 22, 22, 22, 36, 36, 36, 39, 39, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 22, 36, 36, 36, 39, 39, 39, 39, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330404262 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 Building ZINC000330404262 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330404262 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 234) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/234: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)CC1) `ZINC000330404262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330404262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404262 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 10, 12, 12, 12, 12, 24, 24, 24, 37, 37, 37, 37, 37, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 24, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 138 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 235) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/235: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)CC1) `ZINC000330404262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330404262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404262 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 22, 22, 22, 36, 36, 36, 39, 39, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 22, 36, 36, 36, 39, 39, 39, 39, 39, 39, 39, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330404262 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404262 Building ZINC000330404263 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330404263 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/236 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)CC1) `ZINC000330404263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330404263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404263 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 11, 11, 11, 11, 23, 23, 23, 36, 36, 36, 37, 37, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 23, 36, 36, 36, 37, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/237 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)CC1) `ZINC000330404263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330404263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404263 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 21, 21, 21, 33, 33, 33, 35, 35, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 21, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330404263 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 Building ZINC000330404263 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330404263 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 236) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/236: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)CC1) `ZINC000330404263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330404263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404263 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 11, 11, 11, 11, 23, 23, 23, 36, 36, 36, 37, 37, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 23, 36, 36, 36, 37, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 237) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/237: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)CC1) `ZINC000330404263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330404263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330404263 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)N[C@@H](C)C(C)C)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.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 9, 10, 10, 10, 10, 21, 21, 21, 33, 33, 33, 35, 35, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 21, 33, 33, 33, 35, 35, 35, 35, 35, 35, 35, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 135 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330404263 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330404263 Building ZINC000171294884 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171294884 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/238 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/238' -> `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(NC(=O)c2ccoc2C)CC1) `ZINC000171294884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171294884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000171294884 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 18, 18, 18, 39, 39, 39, 39, 39, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 18, 39, 39, 39, 39, 39, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/239 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/239' -> `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(NC(=O)c2ccoc2C)CC1) `ZINC000171294884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171294884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000171294884 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 16, 16, 16, 34, 34, 34, 34, 34, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 16, 34, 34, 34, 34, 34, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171294884 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 Building ZINC000171294884 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171294884 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 238) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)CC1) `ZINC000171294884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171294884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000171294884 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 18, 18, 18, 39, 39, 39, 39, 39, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 18, 39, 39, 39, 39, 39, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 239) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)CC1) `ZINC000171294884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171294884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000171294884 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(NC(=O)c2ccoc2C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 12, 1, 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, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 16, 16, 16, 34, 34, 34, 34, 34, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 7, 7, 16, 34, 34, 34, 34, 34, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171294884 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171294884 Building ZINC000171295935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171295935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/240 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171295935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295935 none O=C([C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 8, 1, 9, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/241 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171295935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295935 none O=C([C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 24, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171295935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 Building ZINC000171295935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171295935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 240) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171295935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295935 none O=C([C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 8, 1, 9, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 241) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171295935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295935 none O=C([C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 11, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 6, 6, 9, 9, 6, 9, 9, 9, 24, 29, 29, 29, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 6, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171295935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295935 Building ZINC000171295940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171295940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/242 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171295940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295940 none O=C([C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 8, 1, 8, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/243 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171295940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295940 none O=C([C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 23, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171295940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 Building ZINC000171295940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171295940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 242) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171295940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295940 none O=C([C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 11, 11, 11, 11, 11, 11, 8, 1, 8, 1, 1, 1, 6, 6, 12, 12, 6, 12, 12, 12, 21, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 11, 11, 6, 12, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 243) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1) `ZINC000171295940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171295940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 56 natoms 55 natoms 54 natoms 53 names: ZINC000171295940 none O=C([C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)N1CCOCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 8, 8, 5, 1, 6, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 23, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 8, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171295940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171295940 Building ZINC000171339623 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171339623 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/244 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171339623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171339623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000171339623 none O=C(CN1CCCC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 30, 30, 30, 30, 30, 11, 11, 11, 5, 2, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/245 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171339623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171339623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000171339623 none O=C(CN1CCCC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 29, 30, 30, 30, 30, 11, 11, 11, 5, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171339623 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 Building ZINC000171339623 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171339623 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 244) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171339623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171339623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000171339623 none O=C(CN1CCCC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 30, 30, 30, 30, 30, 11, 11, 11, 5, 2, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 245) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171339623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171339623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000171339623 none O=C(CN1CCCC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', '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.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 10, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 17, 29, 30, 30, 30, 30, 11, 11, 11, 5, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 29, 29, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171339623 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171339623 Building ZINC000063327247 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000063327247 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/246 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/246' -> `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)NCCCNC(=O)c1ccccc1F) `ZINC000063327247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000063327247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000063327247 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 29, 41, 41, 41, 47, 47, 45, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 20, 20, 27, 28, 41, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/247 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/247' -> `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)NCCCNC(=O)c1ccccc1F) `ZINC000063327247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000063327247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000063327247 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 32, 41, 41, 41, 47, 47, 44, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 21, 21, 29, 30, 41, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000063327247 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 Building ZINC000063327247 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000063327247 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 246) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F) `ZINC000063327247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000063327247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000063327247 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 18, 29, 41, 41, 41, 47, 47, 45, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 20, 20, 27, 28, 41, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 247) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F) `ZINC000063327247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000063327247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000063327247 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCCNC(=O)c1ccccc1F 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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 13, 17, 32, 41, 41, 41, 47, 47, 44, 47, 47, 47, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 21, 21, 29, 30, 41, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000063327247 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000063327247 Building ZINC000330601944 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330601944 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/248 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1) `ZINC000330601944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330601944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000330601944 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 14, 26, 26, 26, 26, 26, 26, 26, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 13, 13, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/249 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1) `ZINC000330601944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330601944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000330601944 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 14, 28, 28, 28, 28, 28, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 15, 15, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330601944 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 Building ZINC000330601944 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330601944 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 248) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/248: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1) `ZINC000330601944.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330601944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000330601944 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 14, 26, 26, 26, 26, 26, 26, 26, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 13, 13, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 249) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/249: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1) `ZINC000330601944.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330601944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000330601944 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCC2CCS(=O)(=O)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 2, 2, 2, 15, 14, 28, 28, 28, 28, 28, 28, 28, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 2, 15, 15, 19, 19, 28, 28, 28, 28, 28, 28, 28, 28, 28, 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]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330601944 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330601944 Building ZINC000171559769 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171559769 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/250 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171559769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171559769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000171559769 none CCN(CC)CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 28, 15, 10, 15, 10, 10, 10, 5, 1, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/251 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171559769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171559769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000171559769 none CCN(CC)CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 29, 17, 11, 17, 11, 11, 11, 5, 2, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 139 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171559769 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 Building ZINC000171559769 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171559769 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 250) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/250: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171559769.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171559769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000171559769 none CCN(CC)CC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 27, 27, 27, 28, 15, 10, 15, 10, 10, 10, 5, 1, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 27, 27, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 251) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000171559769.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171559769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000171559769 none CCN(CC)CC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 28, 29, 17, 11, 17, 11, 11, 11, 5, 2, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 28, 28, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 139 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171559769 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171559769 Building ZINC000330722361 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330722361 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/252 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000330722361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330722361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330722361 none CCN(CC)C(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 16, 17, 17, 6, 16, 6, 6, 6, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 6, 6, 25, 25, 25, 25, 25, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 6] 50 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/253 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000330722361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330722361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330722361 none CCN(CC)C(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 8, 20, 8, 8, 8, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 31, 31, 31, 31, 31, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8, 8, 8] 50 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330722361 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 Building ZINC000330722361 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330722361 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 252) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000330722361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330722361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330722361 none CCN(CC)C(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 16, 17, 17, 6, 16, 6, 6, 6, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 6, 6, 25, 25, 25, 25, 25, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 6, 6, 6, 6] 50 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 253) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000330722361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330722361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000330722361 none CCN(CC)C(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 20, 20, 20, 8, 20, 8, 8, 8, 4, 2, 6, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 8, 8, 31, 31, 31, 31, 31, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 8, 8, 8, 8] 50 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, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330722361 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330722361 Building ZINC000330970172 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330970172 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/254 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O) `ZINC000330970172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330970172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970172 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 18, 12, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 12, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 12, 12, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/255 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O) `ZINC000330970172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330970172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970172 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 12, 12, 16, 12, 6, 2, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 18, 18, 18, 18, 18, 16, 16, 16, 16, 16, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330970172 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 Building ZINC000330970172 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330970172 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 254) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O) `ZINC000330970172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330970172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970172 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 18, 12, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 12, 12, 12, 12, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 12, 12, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 255) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O) `ZINC000330970172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330970172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970172 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 12, 12, 16, 12, 6, 2, 10, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 12, 12, 12, 12, 18, 18, 18, 18, 18, 16, 16, 16, 16, 16, 12, 12, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 124 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330970172 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970172 Building ZINC000330970173 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330970173 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/256 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O) `ZINC000330970173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330970173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970173 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 17, 14, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 14, 14, 14, 14, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 14, 14, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/257 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O) `ZINC000330970173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330970173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970173 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 13, 13, 19, 13, 8, 2, 9, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 13, 13, 13, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 13, 13, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330970173 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 Building ZINC000330970173 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000330970173 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 256) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O) `ZINC000330970173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000330970173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970173 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 14, 14, 17, 14, 10, 2, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 14, 14, 14, 14, 19, 19, 19, 19, 19, 17, 17, 17, 17, 17, 14, 14, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 114 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 257) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O) `ZINC000330970173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000330970173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000330970173 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC[S@@]1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 13, 13, 19, 13, 8, 2, 9, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 13, 13, 13, 13, 21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 13, 13, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000330970173 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000330970173 Building ZINC000927951565 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927951565 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/258 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/258' -> `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)Cc1ccccc1) `ZINC000927951565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927951565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951565 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 26, 35, 11, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 32, 32, 32, 32, 32, 32, 35, 35, 35, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/259 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/259' -> `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)Cc1ccccc1) `ZINC000927951565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927951565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951565 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 21, 33, 8, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 26, 26, 26, 26, 26, 26, 33, 33, 33, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927951565 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 Building ZINC000927951565 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927951565 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 258) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1) `ZINC000927951565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927951565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951565 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 26, 35, 11, 26, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 32, 32, 32, 32, 32, 32, 35, 35, 35, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 259) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1) `ZINC000927951565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927951565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951565 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 21, 33, 8, 21, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 20, 26, 26, 26, 26, 26, 26, 33, 33, 33, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 164 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927951565 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951565 Building ZINC000927951566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927951566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/260 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/260' -> `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)Cc1ccccc1) `ZINC000927951566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927951566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951566 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 8, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 26, 26, 26, 26, 26, 26, 34, 34, 34, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/261 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/261' -> `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)Cc1ccccc1) `ZINC000927951566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927951566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951566 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 23, 33, 11, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 29, 29, 29, 29, 29, 29, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927951566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 Building ZINC000927951566 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927951566 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 260) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1) `ZINC000927951566.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927951566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951566 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 34, 8, 22, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 26, 26, 26, 26, 26, 26, 34, 34, 34, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 26, 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, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 161 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 261) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1) `ZINC000927951566.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927951566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000927951566 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)Cc1ccccc1 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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 23, 33, 11, 23, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 29, 29, 29, 29, 29, 29, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927951566 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927951566 Building ZINC000557127904 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127904 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/262 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127904 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 24, 21, 24, 24, 11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 72, 21, 21, 19, 19, 57, 4, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 282 number of broken/clashed sets: 225 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/263 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127904 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 20, 22, 22, 10, 3, 10, 10, 21, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66, 20, 20, 21, 21, 63, 3, 7, 7, 7, 7, 7, 7, 7] 450 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]) total number of confs: 281 number of broken/clashed sets: 228 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127904 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 Building ZINC000557127904 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127904 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 262) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/262: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127904 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 24, 24, 24, 21, 24, 24, 11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 72, 21, 21, 19, 19, 57, 4, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 282 number of broken/clashed sets: 225 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 263) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127904 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [22, 22, 22, 22, 20, 22, 22, 10, 3, 10, 10, 21, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66, 20, 20, 21, 21, 63, 3, 7, 7, 7, 7, 7, 7, 7] 450 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]) total number of confs: 281 number of broken/clashed sets: 228 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127904 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127904 Building ZINC000557127905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/264 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127905 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 27, 35, 35, 13, 4, 13, 13, 23, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 105, 29, 29, 23, 23, 69, 4, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 385 number of broken/clashed sets: 359 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/265 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127905 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 27, 29, 29, 21, 27, 27, 11, 2, 11, 11, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 81, 22, 22, 21, 21, 63, 2, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 328 number of broken/clashed sets: 232 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 Building ZINC000557127905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 264) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127905 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 35, 35, 35, 27, 35, 35, 13, 4, 13, 13, 23, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 105, 29, 29, 23, 23, 69, 4, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 385 number of broken/clashed sets: 359 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 265) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/265: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127905 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 27, 29, 29, 21, 27, 27, 11, 2, 11, 11, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 81, 22, 22, 21, 21, 63, 2, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 328 number of broken/clashed sets: 232 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127905 Building ZINC000557127907 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127907 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/266 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127907 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 29, 23, 29, 29, 12, 3, 12, 12, 20, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 26, 26, 20, 20, 60, 3, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 326 number of broken/clashed sets: 311 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/267 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127907 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 27, 27, 23, 27, 27, 11, 2, 11, 11, 26, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 23, 23, 26, 26, 78, 2, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 350 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127907 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 Building ZINC000557127907 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557127907 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 266) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/266: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127907.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557127907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127907 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [29, 29, 29, 29, 23, 29, 29, 12, 3, 12, 12, 20, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 26, 26, 20, 20, 60, 3, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 326 number of broken/clashed sets: 311 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 267) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000557127907.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557127907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557127907 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [27, 27, 27, 27, 23, 27, 27, 11, 2, 11, 11, 26, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 23, 23, 26, 26, 78, 2, 6, 6, 6, 6, 6, 6, 6] 450 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]) total number of confs: 350 number of broken/clashed sets: 203 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557127907 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557127907 Building ZINC000557129454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/268 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129454 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [44, 44, 44, 44, 38, 44, 44, 15, 4, 15, 15, 40, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 132, 40, 40, 40, 40, 120, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 264 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/269 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129454 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [46, 46, 46, 46, 39, 46, 46, 19, 5, 19, 19, 42, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 138, 41, 41, 42, 42, 126, 5, 4, 4, 4, 4] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 562 number of broken/clashed sets: 233 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 Building ZINC000557129454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 268) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129454 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [44, 44, 44, 44, 38, 44, 44, 15, 4, 15, 15, 40, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 44, 132, 40, 40, 40, 40, 120, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 560 number of broken/clashed sets: 264 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 269) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/269: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129454 none CC(C)(C)[C@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [46, 46, 46, 46, 39, 46, 46, 19, 5, 19, 19, 42, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 138, 41, 41, 42, 42, 126, 5, 4, 4, 4, 4] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 562 number of broken/clashed sets: 233 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129454 Building ZINC000557129455 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129455 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/270 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129455 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [47, 44, 47, 47, 34, 44, 44, 17, 4, 17, 17, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 132, 35, 35, 34, 34, 102, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 531 number of broken/clashed sets: 271 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/271 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129455 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [50, 49, 50, 50, 39, 49, 49, 19, 4, 19, 19, 39, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 147, 45, 45, 39, 39, 117, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 600 number of broken/clashed sets: 302 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129455 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 Building ZINC000557129455 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129455 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 270) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/270: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129455 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [47, 44, 47, 47, 34, 44, 44, 17, 4, 17, 17, 34, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 47, 47, 47, 47, 47, 47, 47, 47, 47, 132, 35, 35, 34, 34, 102, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 531 number of broken/clashed sets: 271 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 271) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/271: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129455 none CC(C)(C)[C@@H](O)C[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [50, 49, 50, 50, 39, 49, 49, 19, 4, 19, 19, 39, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 50, 147, 45, 45, 39, 39, 117, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 600 number of broken/clashed sets: 302 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129455 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129455 Building ZINC000557129456 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129456 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/272 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129456 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [49, 49, 49, 49, 40, 49, 49, 16, 4, 16, 16, 38, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 40, 40, 38, 38, 114, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 579 number of broken/clashed sets: 276 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/273 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129456 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [48, 48, 48, 48, 38, 48, 48, 18, 4, 18, 18, 35, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 39, 39, 35, 35, 105, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 270 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129456 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 Building ZINC000557129456 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129456 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 272) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/272: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129456.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129456 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [49, 49, 49, 49, 40, 49, 49, 16, 4, 16, 16, 38, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 49, 147, 40, 40, 38, 38, 114, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 579 number of broken/clashed sets: 276 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 273) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/273: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129456.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129456 none CC(C)(C)[C@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [48, 48, 48, 48, 38, 48, 48, 18, 4, 18, 18, 35, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 144, 39, 39, 35, 35, 105, 4, 3, 3, 3, 3] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 270 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129456 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129456 Building ZINC000557129457 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129457 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/274 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129457 none CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [46, 44, 46, 46, 38, 44, 44, 18, 4, 18, 18, 41, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 132, 40, 40, 41, 41, 123, 4, 4, 4, 4, 4] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 242 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/275 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129457 none CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [45, 44, 45, 45, 39, 44, 44, 17, 4, 17, 17, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 132, 41, 41, 42, 42, 126, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 581 number of broken/clashed sets: 270 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129457 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 Building ZINC000557129457 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557129457 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 274) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557129457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129457 none CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [46, 44, 46, 46, 38, 44, 44, 18, 4, 18, 18, 41, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46, 46, 132, 40, 40, 41, 41, 123, 4, 4, 4, 4, 4] 450 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 242 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 275) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000557129457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557129457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557129457 none CC(C)(C)[C@@H](O)C[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 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] 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: [45, 44, 45, 45, 39, 44, 44, 17, 4, 17, 17, 42, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 45, 45, 45, 45, 45, 45, 45, 45, 45, 132, 41, 41, 42, 42, 126, 4, 3, 3, 3, 3] 450 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 581 number of broken/clashed sets: 270 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557129457 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557129457 Building ZINC000628728026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628728026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/276 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/277 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/278 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/278' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/279 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/279' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628728026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 Building ZINC000628728026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628728026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 276) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 277) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 278) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 279) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628728026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 Building ZINC000628728026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628728026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 276) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 277) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 278) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 279) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628728026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 Building ZINC000628728026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628728026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 276) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 277) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 278) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 7, 26, 26, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 26, 3, 3, 3, 3, 3, 3, 4, 26, 26, 26, 26, 50, 50, 50, 26, 26] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 279) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/279: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1) `ZINC000628728026.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628728026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000628728026 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(c2ccc3nncn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 1, 8, 8, 5, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 4, 7, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 4, 23, 23, 23, 23, 50, 50, 50, 23, 23] 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628728026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628728026 Building ZINC000544557139 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544557139 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/280 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000544557139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544557139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544557139 none O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 10, 14, 14, 14, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 10, 10, 42, 16, 16, 50, 50, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/281 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000544557139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544557139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544557139 none O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 8, 13, 13, 13, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 8, 39, 14, 14, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000544557139 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 Building ZINC000544557139 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000544557139 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 280) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000544557139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000544557139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544557139 none O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 10, 14, 14, 14, 16, 28, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 10, 10, 42, 16, 16, 50, 50, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 281) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000544557139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000544557139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000544557139 none O=C(NC[C@H](O)COc1ccc2c(c1)OCO2)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 12, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 8, 13, 13, 13, 14, 27, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 8, 8, 39, 14, 14, 50, 50, 50, 50, 50, 3, 3, 3, 3] 150 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000544557139 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000544557139 Building ZINC001525684700 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525684700 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/282 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1) `ZINC001525684700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525684700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525684700 none COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 34, 47, 34, 34, 15, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 47, 47, 34, 15, 15, 10, 10, 3, 3, 1, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/283 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1) `ZINC001525684700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525684700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525684700 none COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 34, 47, 34, 34, 15, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 47, 47, 34, 15, 15, 10, 10, 3, 3, 1, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525684700 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 Building ZINC001525684700 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525684700 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 282) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1) `ZINC001525684700.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525684700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525684700 none COC(=O)c1cn(CCNC(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 34, 47, 34, 34, 15, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 47, 47, 34, 15, 15, 10, 10, 3, 3, 1, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 283) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1) `ZINC001525684700.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525684700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001525684700 none COC(=O)c1cn(CCNC(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 34, 47, 34, 34, 15, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 34, 34, 47, 47, 47, 34, 15, 15, 10, 10, 3, 3, 1, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525684700 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525684700 Building ZINC000557318656 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557318656 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/284 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557318656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318656 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 20, 12, 20, 20, 45, 45, 45, 20, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 20, 20, 12, 45, 45, 20] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/285 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557318656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318656 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 22, 22, 11, 22, 22, 40, 40, 40, 22, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 22, 22, 13, 40, 40, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557318656 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 Building ZINC000557318656 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557318656 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 284) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/284: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557318656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318656 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 20, 12, 20, 20, 45, 45, 45, 20, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 20, 20, 12, 45, 45, 20] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 285) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/285: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557318656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318656 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 22, 22, 11, 22, 22, 40, 40, 40, 22, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 22, 22, 13, 40, 40, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557318656 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318656 Building ZINC000557318657 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557318657 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/286 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557318657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318657 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 22, 22, 7, 22, 22, 40, 40, 40, 22, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 22, 22, 7, 40, 40, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/287 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557318657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318657 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 20, 7, 20, 20, 44, 44, 44, 20, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 20, 20, 7, 44, 44, 20] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557318657 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 Building ZINC000557318657 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557318657 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 286) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/286: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557318657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318657 none CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 22, 22, 7, 22, 22, 40, 40, 40, 22, 13, 13, 13, 13, 13, 4, 3, 3, 3, 3, 22, 22, 7, 40, 40, 22] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 287) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/287: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1) `ZINC000557318657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557318657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000557318657 none CC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(F)cc1)c1cccc(S(N)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 1, 1, 14, 8, 11, 11, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 7, 20, 20, 7, 20, 20, 44, 44, 44, 20, 9, 9, 9, 9, 9, 4, 3, 3, 3, 3, 20, 20, 7, 44, 44, 20] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557318657 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557318657 Building ZINC000557319192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557319192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/288 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000557319192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557319192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557319192 none O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 49, 49, 50, 50, 49, 50, 50, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/289 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000557319192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557319192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557319192 none O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 22, 22, 22, 22, 49, 49, 50, 50, 49, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557319192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 Building ZINC000557319192 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557319192 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 288) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/288: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000557319192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557319192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557319192 none O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 7, 21, 21, 21, 21, 49, 49, 50, 50, 49, 50, 50, 21, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 289) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/289: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000557319192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557319192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000557319192 none O=C(NC1CCN(C(=O)c2ccncc2)CC1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 6, 22, 22, 22, 22, 49, 49, 50, 50, 49, 50, 50, 22, 22, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 22, 22, 22, 22, 22, 50, 50, 50, 50, 22, 22, 22, 22, 3, 3, 3, 3] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557319192 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557319192 Building ZINC000331150379 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331150379 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/290 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O) `ZINC000331150379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331150379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000331150379 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 19, 16, 7, 2, 12, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 16, 16, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/291 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O) `ZINC000331150379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331150379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000331150379 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 18, 16, 7, 2, 12, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 16, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331150379 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 Building ZINC000331150379 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331150379 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 290) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/290: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O) `ZINC000331150379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331150379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000331150379 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 19, 16, 7, 2, 12, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 16, 16, 16, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 117 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 291) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/291: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O) `ZINC000331150379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331150379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000331150379 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 16, 16, 18, 16, 7, 2, 12, 1, 1, 1, 7, 7, 7, 7, 16, 16, 16, 7, 16, 16, 16, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331150379 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331150379 Building ZINC000557409189 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557409189 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/292 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/292' -> `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)N1CCCC[C@@H]1CCS(C)(=O)=O) `ZINC000557409189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557409189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409189 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/293 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/293' -> `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)N1CCCC[C@@H]1CCS(C)(=O)=O) `ZINC000557409189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557409189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409189 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 20, 20, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 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, 48]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557409189 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 Building ZINC000557409189 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557409189 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 292) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O) `ZINC000557409189.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557409189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409189 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 293) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O) `ZINC000557409189.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557409189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409189 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 20, 20, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 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, 48]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557409189 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409189 Building ZINC000557409190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557409190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/294 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/294' -> `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)N1CCCC[C@H]1CCS(C)(=O)=O) `ZINC000557409190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557409190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409190 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 20, 20, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/295 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/295' -> `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)N1CCCC[C@H]1CCS(C)(=O)=O) `ZINC000557409190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557409190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409190 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557409190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 Building ZINC000557409190 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557409190 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 294) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O) `ZINC000557409190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557409190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409190 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 20, 20, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 37, 37, 37] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 295) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O) `ZINC000557409190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557409190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000557409190 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1CCS(C)(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 5, 14, 5, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 7, 9, 9, 9, 9, 9, 9, 9, 17, 17, 36, 36, 36, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 17, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557409190 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557409190 Building ZINC000331193640 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331193640 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/296 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O) `ZINC000331193640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331193640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000331193640 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 14, 11, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 28 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/297 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O) `ZINC000331193640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331193640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000331193640 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 12, 9, 5, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 23 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331193640 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 Building ZINC000331193640 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331193640 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 296) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O) `ZINC000331193640.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331193640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000331193640 none CCC1(CC)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 11, 11, 11, 14, 11, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 28 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 65 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 297) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O) `ZINC000331193640.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331193640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000331193640 none CCC1(CC)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCS1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 12, 9, 5, 2, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 23 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331193640 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331193640 Building ZINC000172462502 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172462502 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/298 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CCOCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000172462502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172462502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000172462502 none O=C(N1CCN(CC2CCOCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 9, 9, 9, 9, 26, 28, 28, 28, 28, 28, 9, 9, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 9, 9, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/299 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CCOCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000172462502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172462502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000172462502 none O=C(N1CCN(CC2CCOCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172462502 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 Building ZINC000172462502 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172462502 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 298) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CCOCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000172462502.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172462502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000172462502 none O=C(N1CCN(CC2CCOCC2)CC1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 7, 9, 9, 9, 9, 26, 28, 28, 28, 28, 28, 9, 9, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 9, 9, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 299) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC2CCOCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000172462502.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172462502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000172462502 none O=C(N1CCN(CC2CCOCC2)CC1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 8, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 10, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 10, 10, 16, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172462502 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172462502 Building ZINC000273577066 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273577066 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/300 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273577066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577066 none CCNC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 8, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 2, 6, 6, 12, 12, 12, 6, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/301 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273577066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577066 none CCNC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 11, 10, 11, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 5, 5, 10, 27, 27, 27, 27, 27, 11, 10, 10, 10, 10, 2, 5, 5, 11, 11, 11, 5, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273577066 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 Building ZINC000273577066 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273577066 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 300) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273577066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577066 none CCNC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 8, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 6, 6, 2, 6, 12, 6, 6, 6, 8, 26, 26, 26, 26, 26, 8, 8, 8, 8, 8, 2, 6, 6, 12, 12, 12, 6, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 301) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273577066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577066 none CCNC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 11, 10, 11, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 5, 5, 10, 27, 27, 27, 27, 27, 11, 10, 10, 10, 10, 2, 5, 5, 11, 11, 11, 5, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273577066 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577066 Building ZINC000273577074 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273577074 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/302 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273577074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577074 none CCNC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 12, 10, 12, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 10, 27, 27, 27, 27, 27, 12, 10, 10, 10, 10, 2, 4, 4, 8, 8, 8, 4, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/303 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273577074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577074 none CCNC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 11, 8, 11, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 8, 27, 27, 27, 27, 27, 11, 8, 8, 8, 8, 2, 4, 4, 8, 8, 8, 4, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273577074 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 Building ZINC000273577074 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273577074 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 302) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/302: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273577074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577074 none CCNC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 12, 12, 10, 12, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 10, 27, 27, 27, 27, 27, 12, 10, 10, 10, 10, 2, 4, 4, 8, 8, 8, 4, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 303) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/303: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1) `ZINC000273577074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273577074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000273577074 none CCNC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 11, 11, 8, 11, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 8, 27, 27, 27, 27, 27, 11, 8, 8, 8, 8, 2, 4, 4, 8, 8, 8, 4, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273577074 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273577074 Building ZINC000273586105 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273586105 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/304 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl) `ZINC000273586105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273586105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000273586105 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 12, 12, 12, 12, 18, 18, 25, 25, 12, 12, 6, 6, 6, 9, 9, 9, 6, 6, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 12, 12, 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]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/305 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl) `ZINC000273586105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273586105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000273586105 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [11, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 14, 14, 14, 14, 18, 18, 24, 24, 14, 14, 6, 6, 6, 11, 11, 11, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273586105 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 Building ZINC000273586105 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273586105 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 304) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/304: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl) `ZINC000273586105.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273586105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000273586105 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 12, 12, 12, 12, 18, 18, 25, 25, 12, 12, 6, 6, 6, 9, 9, 9, 6, 6, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 12, 12, 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]) total number of confs: 109 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 305) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/305: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl) `ZINC000273586105.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273586105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000273586105 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)C(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [11, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 14, 14, 14, 14, 18, 18, 24, 24, 14, 14, 6, 6, 6, 11, 11, 11, 6, 6, 14, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 14, 14, 14, 14, 6] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273586105 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273586105 Building ZINC000557686287 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557686287 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/306 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557686287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686287 none CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 26, 23, 23, 23, 23, 23, 14, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/307 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557686287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686287 none CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens 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, 24, 25, 25, 24, 24, 24, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557686287 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 Building ZINC000557686287 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557686287 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 306) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/306: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557686287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686287 none CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 26, 26, 23, 23, 23, 23, 23, 14, 23, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 307) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557686287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686287 none CS(=O)(=O)N1CCCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens 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, 24, 25, 25, 24, 24, 24, 24, 24, 13, 24, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557686287 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686287 Building ZINC000557686288 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557686288 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/308 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557686288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686288 none CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 26, 26, 24, 24, 24, 24, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/309 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557686288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686288 none CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 24, 20, 20, 20, 20, 20, 12, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557686288 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 Building ZINC000557686288 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557686288 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 308) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557686288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686288 none CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 24, 26, 26, 24, 24, 24, 24, 24, 14, 24, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 26, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 309) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/309: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000557686288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557686288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000557686288 none CS(=O)(=O)N1CCCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 8, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 20, 24, 24, 20, 20, 20, 20, 20, 12, 20, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/335759/xcu-8058115.73/working/building/ZINC000557686288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557686288 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557686288 Building ZINC000557690158 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557690158 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/310 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000557690158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557690158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000557690158 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 17, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 17, 32, 32, 17, 17, 3, 3] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/311 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000557690158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557690158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000557690158 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 11, 16, 16, 16, 16, 30, 30, 30, 30, 16, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 16, 16, 30, 30, 16, 16, 3, 3] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557690158 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 Building ZINC000557690158 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000557690158 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 310) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/310: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000557690158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000557690158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000557690158 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 17, 17, 17, 17, 32, 32, 32, 32, 17, 17, 17, 1, 1, 1, 3, 3, 3, 3, 3, 17, 17, 17, 17, 32, 32, 17, 17, 3, 3] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 311) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/311: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000557690158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000557690158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000557690158 none O=C(N1CCN(CC(F)(F)F)C(=O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 5, 5, 15, 15, 15, 1, 11, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 11, 16, 16, 16, 16, 30, 30, 30, 30, 16, 16, 16, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 16, 16, 30, 30, 16, 16, 3, 3] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000557690158 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000557690158 Building ZINC000273629872 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273629872 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/312 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273629872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629872 none CC[C@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 5, 15, 15, 21, 5, 5, 5, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 5, 5, 19, 19, 19, 19, 19, 21, 21, 63, 5, 5, 5, 5, 6, 6, 11, 11, 11, 6, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/313 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273629872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629872 none CC[C@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 20, 20, 26, 8, 8, 8, 4, 1, 2, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 8, 8, 22, 22, 22, 22, 22, 26, 26, 78, 8, 8, 8, 8, 3, 3, 7, 7, 7, 3, 8, 8, 8, 8] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273629872 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 Building ZINC000273629872 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273629872 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 312) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629872.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273629872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629872 none CC[C@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 5, 15, 15, 21, 5, 5, 5, 3, 1, 2, 1, 1, 1, 6, 6, 2, 6, 11, 6, 6, 6, 5, 5, 19, 19, 19, 19, 19, 21, 21, 63, 5, 5, 5, 5, 6, 6, 11, 11, 11, 6, 5, 5, 5, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 313) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629872.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273629872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629872 none CC[C@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 20, 20, 26, 8, 8, 8, 4, 1, 2, 1, 1, 1, 3, 3, 2, 3, 7, 3, 3, 3, 8, 8, 22, 22, 22, 22, 22, 26, 26, 78, 8, 8, 8, 8, 3, 3, 7, 7, 7, 3, 8, 8, 8, 8] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 202 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273629872 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629872 Building ZINC000273629878 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273629878 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/314 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273629878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629878 none CC[C@@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 19, 19, 25, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 7, 7, 22, 22, 22, 22, 22, 25, 25, 75, 7, 7, 7, 7, 4, 4, 8, 8, 8, 4, 7, 7, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/315 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/315' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273629878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629878 none CC[C@@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 19, 19, 24, 9, 9, 9, 4, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 9, 9, 22, 22, 22, 22, 22, 24, 24, 72, 9, 9, 9, 9, 4, 4, 8, 8, 8, 4, 9, 9, 9, 9] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273629878 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 Building ZINC000273629878 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273629878 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 314) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273629878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629878 none CC[C@@H](CO)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 19, 19, 25, 7, 7, 7, 4, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 7, 7, 22, 22, 22, 22, 22, 25, 25, 75, 7, 7, 7, 7, 4, 4, 8, 8, 8, 4, 7, 7, 7, 7] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 203 number of broken/clashed sets: 69 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 315) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000273629878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273629878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273629878 none CC[C@@H](CO)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 9, 19, 19, 24, 9, 9, 9, 4, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 9, 9, 22, 22, 22, 22, 22, 24, 24, 72, 9, 9, 9, 9, 4, 4, 8, 8, 8, 4, 9, 9, 9, 9] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273629878 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273629878 Building ZINC000273699452 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273699452 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/316 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273699452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699452 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 11, 24, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 24, 24, 24, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/317 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273699452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699452 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 22, 22, 22, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273699452 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 Building ZINC000273699452 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273699452 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 316) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273699452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699452 none COC(=O)[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 11, 24, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 24, 24, 24, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 317) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273699452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699452 none COC(=O)[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 22, 22, 22, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273699452 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699452 Building ZINC000273699455 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273699455 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/318 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273699455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699455 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 22, 22, 22, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/319 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273699455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699455 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 11, 24, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 24, 24, 24, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273699455 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 Building ZINC000273699455 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273699455 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 318) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/318: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699455.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273699455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699455 none COC(=O)[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 22, 22, 22, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 319) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/319: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1) `ZINC000273699455.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273699455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000273699455 none COC(=O)[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CCSC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 14, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 11, 24, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 11, 11, 11, 11, 24, 24, 24, 3, 4, 4, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273699455 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273699455 Building ZINC000172849614 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172849614 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/320 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172849614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849614 none Cn1ccc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 23, 23, 23, 23, 23, 4, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/321 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172849614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849614 none Cn1ccc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 24, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172849614 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 Building ZINC000172849614 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172849614 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 320) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/320: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172849614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849614 none Cn1ccc(N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 23, 23, 23, 23, 23, 4, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 24, 24, 24, 24, 24, 24, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 321) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/321: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172849614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849614 none Cn1ccc(N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 24, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172849614 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849614 Building ZINC000172849617 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172849617 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/322 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172849617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849617 none Cn1ccc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 26, 26, 26, 26, 7, 26, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 27, 27, 27, 27, 27, 27, 26, 26, 26, 26, 26, 26, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/323 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172849617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849617 none Cn1ccc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 23, 23, 23, 23, 23, 6, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172849617 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 Building ZINC000172849617 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172849617 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 322) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849617.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172849617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849617 none Cn1ccc(N2CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 26, 26, 26, 26, 26, 7, 26, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 26, 26, 27, 27, 27, 27, 27, 27, 26, 26, 26, 26, 26, 26, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 323) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1) `ZINC000172849617.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172849617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000172849617 none Cn1ccc(N2CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 23, 23, 23, 23, 23, 6, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 23, 23, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172849617 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172849617 Building ZINC000273920779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273920779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/324 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl) `ZINC000273920779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273920779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000273920779 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 7, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/325 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl) `ZINC000273920779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273920779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000273920779 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 7, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273920779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 Building ZINC000273920779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273920779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 324) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/324: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl) `ZINC000273920779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273920779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000273920779 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 7, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 325) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/325: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl) `ZINC000273920779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273920779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000273920779 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCS(=O)(=O)C(C)(C)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 11, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 2, 7, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273920779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273920779 Building ZINC000173015720 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173015720 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/326 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173015720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015720 none Cc1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/327 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173015720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015720 none Cc1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000173015720 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 Building ZINC000173015720 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173015720 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 326) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173015720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015720 none Cc1cc(N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 327) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173015720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015720 none Cc1cc(N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000173015720 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015720 Building ZINC000173015725 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173015725 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/328 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173015725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015725 none Cc1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/329 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173015725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015725 none Cc1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000173015725 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 Building ZINC000173015725 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000173015725 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 328) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000173015725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015725 none Cc1cc(N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 59 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 329) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1) `ZINC000173015725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000173015725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000173015725 none Cc1cc(N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)C2=O)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 25, 25, 25, 25, 25, 25, 25, 10, 10, 10, 10, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000173015725 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000173015725 Building ZINC000273967226 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967226 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/330 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000273967226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967226 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 6, 7, 9, 9, 9, 9, 9, 9, 9, 17, 24, 24, 24, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 17, 17, 72, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 217 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/331 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000273967226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967226 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 8, 8, 8, 18, 28, 28, 28, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 18, 18, 84, 42, 42, 42] 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]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967226 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 Building ZINC000273967226 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967226 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 330) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/330: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000273967226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967226 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 6, 7, 9, 9, 9, 9, 9, 9, 9, 17, 24, 24, 24, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 17, 17, 72, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 217 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 331) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1) `ZINC000273967226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967226 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 8, 8, 8, 18, 28, 28, 28, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 18, 18, 84, 42, 42, 42] 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]) total number of confs: 232 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967226 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967226 Building ZINC000273967232 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967232 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/332 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000273967232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967232 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 17, 27, 27, 27, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 17, 17, 81, 42, 42, 42] 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]) total number of confs: 242 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/333 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/333' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000273967232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967232 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 16, 23, 23, 23, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 16, 69, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967232 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 Building ZINC000273967232 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967232 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 332) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000273967232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967232 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 17, 27, 27, 27, 42, 42, 42, 42, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 17, 17, 81, 42, 42, 42] 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]) total number of confs: 242 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 333) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1) `ZINC000273967232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967232 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 2, 7, 8, 9, 9, 9, 9, 9, 9, 9, 16, 23, 23, 23, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 16, 69, 40, 40, 40] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 210 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967232 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967232 Building ZINC000273967237 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967237 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/334 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000273967237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967237 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 8, 8, 8, 15, 29, 29, 29, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 87, 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]) total number of confs: 247 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/335 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000273967237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967237 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 7, 12, 19, 19, 19, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 12, 12, 57, 44, 44, 44] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967237 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 Building ZINC000273967237 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967237 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 334) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/334: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000273967237.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967237 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 4, 5, 8, 8, 8, 8, 8, 8, 8, 15, 29, 29, 29, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 15, 15, 87, 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]) total number of confs: 247 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 335) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/335: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1) `ZINC000273967237.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967237 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@H]1C[C@@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 7, 12, 19, 19, 19, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 12, 12, 57, 44, 44, 44] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967237 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967237 Building ZINC000273967240 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967240 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/336 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000273967240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967240 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 7, 12, 21, 21, 21, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 12, 12, 63, 47, 47, 47] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/337 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/337' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000273967240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967240 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 16, 30, 30, 30, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 16, 90, 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]) total number of confs: 237 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967240 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 Building ZINC000273967240 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000273967240 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 336) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000273967240.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000273967240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967240 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 2, 5, 6, 7, 7, 7, 7, 7, 7, 7, 12, 21, 21, 21, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 12, 12, 63, 47, 47, 47] 150 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 337) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1) `ZINC000273967240.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000273967240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000273967240 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCOC[C@@H]1C[C@H](O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 5, 5, 7, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 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] 1 hydrogens 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, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 16, 30, 30, 30, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 16, 16, 90, 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]) total number of confs: 237 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000273967240 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000273967240 Building ZINC000274050632 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274050632 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/338 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl) `ZINC000274050632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274050632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000274050632 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 4, 8, 11, 11, 11, 11, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 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]) total number of confs: 48 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/339 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl) `ZINC000274050632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274050632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000274050632 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 5, 8, 11, 11, 11, 11, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274050632 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 Building ZINC000274050632 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274050632 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 338) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl) `ZINC000274050632.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274050632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000274050632 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 4, 8, 11, 11, 11, 11, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 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]) total number of confs: 48 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 339) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/339: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl) `ZINC000274050632.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274050632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000274050632 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cccnn3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 2, 5, 8, 11, 11, 11, 11, 27, 27, 27, 27, 27, 11, 11, 2, 2, 2, 4, 4, 4, 2, 2, 11, 11, 11, 11, 27, 27, 27, 11, 11, 11, 11, 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]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274050632 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274050632 Building ZINC000461144987 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461144987 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/340 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1) `ZINC000461144987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461144987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000461144987 none COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 19, 19, 19, 19, 7, 1, 10, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 19, 19, 49, 49, 49, 50, 50, 50, 49, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 49] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/341 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/341' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1) `ZINC000461144987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461144987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000461144987 none COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 17, 17, 17, 17, 8, 2, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 46, 46, 46, 48, 48, 48, 46, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 46] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461144987 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 Building ZINC000461144987 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461144987 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 340) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/340: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1) `ZINC000461144987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461144987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000461144987 none COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 19, 19, 19, 19, 7, 1, 10, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 19, 19, 49, 49, 49, 50, 50, 50, 49, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 49] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 341) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/341: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1) `ZINC000461144987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461144987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000461144987 none COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 46, 17, 17, 17, 17, 8, 2, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 46, 46, 46, 48, 48, 48, 46, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 46] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461144987 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461144987 Building ZINC000274105012 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274105012 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/342 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl) `ZINC000274105012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274105012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274105012 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 5, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 27, 27, 27, 27, 27, 10, 10, 10, 10, 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/343 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl) `ZINC000274105012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274105012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274105012 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 5, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 9, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 9, 9, 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]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274105012 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 Building ZINC000274105012 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274105012 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 342) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/342: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl) `ZINC000274105012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274105012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274105012 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 5, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 10, 10, 10, 10, 27, 27, 27, 27, 27, 27, 10, 10, 2, 2, 2, 4, 4, 4, 2, 2, 10, 10, 10, 10, 27, 27, 27, 27, 27, 10, 10, 10, 10, 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]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 343) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/343: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl) `ZINC000274105012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274105012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274105012 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3ccnc(C)n3)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 1, 5, 8, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 2, 1, 1, 1, 1, 5, 8, 9, 9, 9, 9, 26, 26, 26, 26, 26, 26, 9, 9, 2, 2, 2, 4, 4, 4, 2, 2, 9, 9, 9, 9, 26, 26, 26, 26, 26, 9, 9, 9, 9, 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]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274105012 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274105012 Building ZINC000274137401 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274137401 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/344 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl) `ZINC000274137401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274137401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274137401 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 5, 3, 5, 5, 1, 1, 1, 2, 4, 8, 9, 9, 9, 9, 24, 24, 25, 25, 9, 9, 5, 5, 5, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 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]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/345 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl) `ZINC000274137401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274137401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274137401 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 6, 6, 6, 9, 9, 9, 6, 6, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 11, 11, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274137401 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 Building ZINC000274137401 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274137401 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 344) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/344: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl) `ZINC000274137401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274137401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274137401 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 5, 3, 5, 5, 1, 1, 1, 2, 4, 8, 9, 9, 9, 9, 24, 24, 25, 25, 9, 9, 5, 5, 5, 9, 9, 9, 5, 5, 9, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 9, 9, 9, 9, 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]) total number of confs: 86 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 345) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/345: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl) `ZINC000274137401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274137401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274137401 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(C(=O)N(C)C)CC2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 5, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 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: [9, 6, 2, 6, 6, 1, 1, 1, 2, 4, 8, 11, 11, 11, 11, 24, 24, 24, 24, 11, 11, 6, 6, 6, 9, 9, 9, 6, 6, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 11, 11, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274137401 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274137401 Building ZINC000461169501 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461169501 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/346 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1) `ZINC000461169501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461169501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000461169501 none COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 50] 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: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/347 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1) `ZINC000461169501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461169501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000461169501 none COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 15, 15, 15, 15, 8, 2, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 50] 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461169501 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 Building ZINC000461169501 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461169501 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 346) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/346: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1) `ZINC000461169501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461169501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000461169501 none COc1cc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 16, 16, 16, 16, 8, 2, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 50] 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: 87 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 347) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/347: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1) `ZINC000461169501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461169501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000461169501 none COc1cc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cc(F)ccc3C)CC2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 15, 15, 15, 15, 8, 2, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 50] 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: 83 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461169501 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461169501 Building ZINC000274126465 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274126465 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/348 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/349 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/349' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/350 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/350' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/351 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/351' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274126465 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 Building ZINC000274126465 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274126465 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 348) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 349) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 350) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 351) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274126465 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 Building ZINC000274126465 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274126465 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 348) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 349) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 350) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 351) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274126465 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 Building ZINC000274126465 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000274126465 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 348) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 349) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 19, 11, 11, 11, 11, 11, 6, 1, 9, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 29, 29, 29, 20, 20, 19, 19, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 350) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/350: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 351) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/351: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274126465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000274126465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000274126465 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 20, 11, 11, 11, 11, 11, 6, 1, 8, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 11, 11, 28, 28, 28, 21, 21, 20, 20, 11, 11, 11, 11, 11, 11, 2, 2, 5, 5, 5, 2, 11, 11, 11, 11] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274126465 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274126465 Building ZINC000274142496 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274142496 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/352 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000274142496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274142496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000274142496 none COc1ccnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 18, 18, 18, 18, 6, 2, 9, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 18, 18, 46, 46, 46, 46, 46, 46, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/353 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000274142496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274142496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000274142496 none COc1ccnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 16, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274142496 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 Building ZINC000274142496 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274142496 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 352) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000274142496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274142496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000274142496 none COc1ccnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 18, 18, 18, 18, 6, 2, 9, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 18, 18, 46, 46, 46, 46, 46, 46, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 353) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/353: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000274142496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274142496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000274142496 none COc1ccnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 16, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274142496 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274142496 Building ZINC000274165680 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274165680 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/354 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274165680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274165680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274165680 none CCOC(=O)C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7] 1 hydrogens 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, 19, 19, 7, 19, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 7, 7, 30, 30, 30, 30, 30, 21, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 7, 7, 7, 7] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/355 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274165680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274165680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274165680 none CCOC(=O)C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7] 1 hydrogens 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, 20, 7, 20, 7, 7, 7, 7, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 7, 7, 28, 28, 28, 28, 28, 21, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 7, 7, 7, 7] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274165680 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 Building ZINC000274165680 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274165680 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 354) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/354: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274165680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274165680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274165680 none CCOC(=O)C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7] 1 hydrogens 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, 19, 19, 7, 19, 7, 7, 7, 7, 5, 2, 6, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 7, 7, 30, 30, 30, 30, 30, 21, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 7, 7, 7, 7] 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 355) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1) `ZINC000274165680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274165680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000274165680 none CCOC(=O)C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 7] 1 hydrogens 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, 20, 7, 20, 7, 7, 7, 7, 4, 2, 5, 1, 1, 1, 2, 2, 2, 2, 4, 2, 2, 2, 7, 7, 28, 28, 28, 28, 28, 21, 7, 7, 7, 7, 2, 2, 4, 4, 4, 2, 7, 7, 7, 7] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274165680 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274165680 Building ZINC000628827737 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628827737 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/356 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/356' -> `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)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 22, 33, 33, 33, 33, 33, 33, 33, 43, 43, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 22, 22, 33, 33, 33, 33, 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, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/357 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/357' -> `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)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 17, 21, 34, 34, 34, 34, 34, 34, 34, 44, 44, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 17, 17, 21, 21, 34, 34, 34, 34, 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, 50, 51]) total number of confs: 160 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/358 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/358' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 30, 42, 42, 42, 42, 42, 42, 42, 45, 45, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 42, 42, 42, 42, 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, 50, 51]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/359 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/359' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 44, 44, 44, 44, 44, 44, 44, 47, 47, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 32, 32, 44, 44, 44, 44, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628827737 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 Building ZINC000628827737 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628827737 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 356) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 22, 33, 33, 33, 33, 33, 33, 33, 43, 43, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 22, 22, 33, 33, 33, 33, 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, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 357) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 17, 21, 34, 34, 34, 34, 34, 34, 34, 44, 44, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 17, 17, 21, 21, 34, 34, 34, 34, 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, 50, 51]) total number of confs: 160 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 358) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 30, 42, 42, 42, 42, 42, 42, 42, 45, 45, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 42, 42, 42, 42, 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, 50, 51]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 359) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 44, 44, 44, 44, 44, 44, 44, 47, 47, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 32, 32, 44, 44, 44, 44, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628827737 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 Building ZINC000628827737 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628827737 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 356) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 22, 33, 33, 33, 33, 33, 33, 33, 43, 43, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 22, 22, 33, 33, 33, 33, 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, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 357) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 17, 21, 34, 34, 34, 34, 34, 34, 34, 44, 44, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 17, 17, 21, 21, 34, 34, 34, 34, 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, 50, 51]) total number of confs: 160 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 358) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 30, 42, 42, 42, 42, 42, 42, 42, 45, 45, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 42, 42, 42, 42, 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, 50, 51]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 359) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 44, 44, 44, 44, 44, 44, 44, 47, 47, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 32, 32, 44, 44, 44, 44, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628827737 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 Building ZINC000628827737 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628827737 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 356) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 18, 22, 33, 33, 33, 33, 33, 33, 33, 43, 43, 33, 33, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 18, 18, 22, 22, 33, 33, 33, 33, 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, 50, 51]) total number of confs: 159 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 357) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1/cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 17, 21, 34, 34, 34, 34, 34, 34, 34, 44, 44, 34, 34, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 17, 17, 21, 21, 34, 34, 34, 34, 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, 50, 51]) total number of confs: 160 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 358) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/358: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 30, 42, 42, 42, 42, 42, 42, 42, 45, 45, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 42, 42, 42, 42, 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, 50, 51]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 359) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/359: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1) `ZINC000628827737.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628827737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000628827737 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC/N=c1\cc(C)nc(C(C)C)[nH]-1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 8, 1, 5, 5, 5, 8, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 44, 44, 44, 44, 44, 44, 44, 47, 47, 44, 44, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 32, 32, 44, 44, 44, 44, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 180 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628827737 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628827737 Building ZINC000274188251 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274188251 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/360 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1) `ZINC000274188251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274188251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000274188251 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 29, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 24, 25, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/361 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1) `ZINC000274188251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274188251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000274188251 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 28, 50, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 24, 25, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274188251 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 Building ZINC000274188251 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274188251 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 360) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1) `ZINC000274188251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274188251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000274188251 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 22, 29, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 24, 25, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 361) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1) `ZINC000274188251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274188251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000274188251 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2cnc(N3CCOCC3)c(F)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 28, 50, 50, 50, 50, 50, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 24, 25, 26, 27, 28, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274188251 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274188251 Building ZINC000776962280 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776962280 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/362 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776962280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962280 none COC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 18, 29, 18, 18, 18, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 18, 18, 29, 29, 29, 18, 18, 18, 18, 18, 6, 6, 6, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/363 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/363' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776962280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962280 none COC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 20, 29, 20, 20, 20, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 20, 20, 29, 29, 29, 20, 20, 20, 20, 20, 6, 6, 6, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776962280 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 Building ZINC000776962280 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776962280 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 362) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776962280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962280 none COC(=O)N1CCC([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 18, 29, 18, 18, 18, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 18, 18, 29, 29, 29, 18, 18, 18, 18, 18, 6, 6, 6, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 18] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 363) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776962280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962280 none COC(=O)N1CCC([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 20, 29, 20, 20, 20, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 20, 20, 29, 29, 29, 20, 20, 20, 20, 20, 6, 6, 6, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 20, 20, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776962280 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962280 Building ZINC000776962282 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776962282 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/364 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776962282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962282 none COC(=O)N1CCC([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 20, 27, 20, 20, 20, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 20, 20, 27, 27, 27, 20, 20, 20, 20, 20, 6, 6, 6, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 20, 20, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/365 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776962282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962282 none COC(=O)N1CCC([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 22, 29, 22, 22, 22, 11, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 29, 29, 29, 22, 22, 22, 22, 22, 7, 7, 7, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 22, 22, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776962282 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 Building ZINC000776962282 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000776962282 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 364) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000776962282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962282 none COC(=O)N1CCC([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 20, 27, 20, 20, 20, 10, 2, 6, 6, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 20, 20, 27, 27, 27, 20, 20, 20, 20, 20, 6, 6, 6, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 20, 20, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 365) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)N1CCC([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC000776962282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000776962282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000776962282 none COC(=O)N1CCC([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 22, 29, 22, 22, 22, 11, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 29, 29, 29, 22, 22, 22, 22, 22, 7, 7, 7, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 22, 22, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000776962282 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000776962282 Building ZINC000274205991 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274205991 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/366 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1) `ZINC000274205991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274205991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274205991 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 28, 50, 50, 50, 50, 50, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/367 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1) `ZINC000274205991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274205991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274205991 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 28, 50, 50, 50, 50, 50, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274205991 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 Building ZINC000274205991 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274205991 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 366) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/366: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1) `ZINC000274205991.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274205991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274205991 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 28, 50, 50, 50, 50, 50, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 367) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/367: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1) `ZINC000274205991.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274205991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274205991 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnc(N2CCOCC2)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 28, 50, 50, 50, 50, 50, 25, 25, 25, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 25, 50, 50, 50, 50, 50, 50, 50, 50, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274205991 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274205991 Building ZINC000461280933 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280933 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/368 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280933 none COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/369 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280933 none COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 4, 9, 9, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280933 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 Building ZINC000461280933 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280933 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 368) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280933 none COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 369) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280933 none COC(=O)[C@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 4, 9, 9, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280933 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280933 Building ZINC000461280934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/370 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280934 none COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/371 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280934 none COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 4, 7, 7, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 Building ZINC000461280934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 370) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280934 none COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 371) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/371: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280934 none COC(=O)[C@@H](C[C@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 4, 7, 7, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280934 Building ZINC000461280935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/372 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280935 none COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 4, 9, 9, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/373 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280935 none COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 Building ZINC000461280935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 372) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280935 none COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 19, 4, 9, 9, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 19, 17, 17, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 373) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280935 none COC(=O)[C@@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 17, 2, 8, 8, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 15, 15, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280935 Building ZINC000461280936 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280936 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/374 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280936 none COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/375 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280936 none COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280936 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 Building ZINC000461280936 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461280936 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 374) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/374: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280936.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280936 none COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 15, 15, 15, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 375) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/375: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000461280936.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461280936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000461280936 none COC(=O)[C@H](C[C@@H]1CCCc2ccccc21)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 4, 7, 7, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6] 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]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461280936 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461280936 Building ZINC000331829226 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331829226 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/376 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1) `ZINC000331829226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331829226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829226 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 9, 20, 31, 31, 31, 31, 31, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 9, 9, 9, 9, 9, 9, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/377 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1) `ZINC000331829226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331829226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829226 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 11, 11, 22, 31, 31, 31, 31, 31, 11, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 11, 11, 11, 11, 11, 11, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331829226 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 Building ZINC000331829226 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331829226 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 376) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/376: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1) `ZINC000331829226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331829226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829226 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 9, 20, 31, 31, 31, 31, 31, 9, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 9, 9, 9, 9, 9, 9, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 124 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 377) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/377: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1) `ZINC000331829226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331829226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829226 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 5, 9, 11, 11, 11, 11, 11, 11, 22, 31, 31, 31, 31, 31, 11, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 11, 11, 11, 11, 11, 11, 22, 22, 31, 31, 31, 31, 31, 31, 31, 31, 11, 11, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331829226 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829226 Building ZINC000331829228 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331829228 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/378 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1) `ZINC000331829228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331829228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829228 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 5, 9, 12, 12, 12, 12, 12, 12, 23, 32, 32, 32, 32, 32, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/379 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1) `ZINC000331829228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331829228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829228 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 11, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331829228 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 Building ZINC000331829228 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000331829228 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 378) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1) `ZINC000331829228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000331829228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829228 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 5, 9, 12, 12, 12, 12, 12, 12, 23, 32, 32, 32, 32, 32, 12, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 12, 12, 12, 12, 12, 12, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 379) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1) `ZINC000331829228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000331829228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000331829228 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCC[C@H](CN3CCOCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 11, 5, 5, 1, 1, 1, 2, 5, 7, 11, 11, 11, 11, 11, 11, 23, 32, 32, 32, 32, 32, 11, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 11, 11, 11, 11, 11, 11, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 11, 11, 5] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 130 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000331829228 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000331829228 Building ZINC000461348353 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348353 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/380 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348353 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 13, 2, 16, 1, 1, 1, 5, 5, 2, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31, 31, 31, 31] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/381 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348353 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 10, 2, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25, 25, 25, 25] 28 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348353 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 Building ZINC000461348353 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348353 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 380) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348353 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 13, 2, 16, 1, 1, 1, 5, 5, 2, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 31, 31, 31, 31, 31] 32 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 381) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348353 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 10, 2, 14, 1, 1, 1, 5, 5, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 25, 25, 25, 25, 25] 28 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348353 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348353 Building ZINC000461348354 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348354 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/382 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O) `ZINC000461348354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348354 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 13, 2, 13, 1, 1, 1, 4, 4, 1, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 25, 25, 25, 25, 25] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/383 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/383' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O) `ZINC000461348354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348354 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 24, 24, 24, 24, 24] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348354 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 Building ZINC000461348354 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348354 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 382) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O) `ZINC000461348354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348354 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 13, 2, 13, 1, 1, 1, 4, 4, 1, 4, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 25, 25, 25, 25, 25] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 383) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O) `ZINC000461348354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348354 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 24, 24, 24, 24, 24] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348354 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348354 Building ZINC000461348356 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348356 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/384 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348356 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 1, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 24, 24, 24, 24, 24] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/385 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348356 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 25, 25, 25, 25, 25] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348356 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 Building ZINC000461348356 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461348356 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 384) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461348356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348356 none C[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 15, 2, 15, 1, 1, 1, 4, 4, 1, 4, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4, 24, 24, 24, 24, 24] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 385) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O) `ZINC000461348356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461348356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461348356 none C[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C[C@H](C)S1(=O)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'S.o2', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 5, 14, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 15, 2, 15, 1, 1, 1, 4, 4, 1, 1, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 4, 4, 4, 25, 25, 25, 25, 25] 27 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461348356 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461348356 Building ZINC000461461902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461461902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/386 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000461461902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461461902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461461902 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 31, 18, 31, 31, 18, 5, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 49, 49, 49, 49, 18, 18, 36, 4, 5, 5, 5, 5, 18] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/387 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/387' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000461461902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461461902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461461902 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 37, 22, 37, 37, 22, 13, 22, 22, 22, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 22, 49, 49, 49, 49, 22, 22, 44, 4, 4, 4, 4, 4, 22] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461461902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 Building ZINC000461461902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461461902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 386) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000461461902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461461902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461461902 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 31, 18, 31, 31, 18, 5, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 1, 5, 5, 18, 49, 49, 49, 49, 18, 18, 36, 4, 5, 5, 5, 5, 18] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 387) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000461461902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461461902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461461902 none CNS(=O)(=O)c1ccc(O)c(NC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 37, 22, 37, 37, 22, 13, 22, 22, 22, 4, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 22, 49, 49, 49, 49, 22, 22, 44, 4, 4, 4, 4, 4, 22] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 269 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461461902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461461902 Building ZINC000461510905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461510905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/388 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461510905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510905 none O=C(N[C@@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 12, 12, 25, 30, 17, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 29, 30, 90, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/389 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461510905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510905 none O=C(N[C@@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 11, 11, 23, 32, 15, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 25, 25, 32, 32, 96, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 332 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461510905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 Building ZINC000461510905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461510905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 388) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/388: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461510905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510905 none O=C(N[C@@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 12, 12, 25, 30, 17, 42, 42, 42, 42, 42, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 26, 26, 29, 30, 90, 42, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 389) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/389: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461510905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510905 none O=C(N[C@@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 11, 11, 23, 32, 15, 38, 38, 38, 38, 38, 1, 1, 1, 3, 3, 1, 2, 3, 3, 4, 25, 25, 32, 32, 96, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 332 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461510905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510905 Building ZINC000461510906 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461510906 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/390 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461510906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510906 none O=C(N[C@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 11, 11, 25, 33, 15, 39, 39, 39, 39, 39, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 27, 27, 33, 33, 99, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 338 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/391 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/391' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461510906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510906 none O=C(N[C@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 12, 12, 23, 30, 16, 40, 40, 40, 40, 40, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 24, 24, 30, 29, 90, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461510906 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 Building ZINC000461510906 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461510906 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 390) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461510906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510906 none O=C(N[C@H](CCO)C1CCOCC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 11, 11, 25, 33, 15, 39, 39, 39, 39, 39, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 27, 27, 33, 33, 99, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 338 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 391) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000461510906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461510906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000461510906 none O=C(N[C@H](CCO)C1CCOCC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 12, 12, 23, 30, 16, 40, 40, 40, 40, 40, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 24, 24, 30, 29, 90, 40, 40, 40, 40, 40, 40, 40, 40, 40, 3, 3, 3, 3] 150 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 306 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461510906 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461510906 Building ZINC000461512010 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461512010 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/392 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461512010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512010 none CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/393 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461512010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512010 none CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [43, 23, 43, 43, 23, 23, 23, 23, 23, 12, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 43, 43, 43, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23] 45 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461512010 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 Building ZINC000461512010 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461512010 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 392) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/392: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461512010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512010 none CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36] set([0, 2, 3, 22, 23, 24]) total number of confs: 7 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 393) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461512010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512010 none CS(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [43, 23, 43, 43, 23, 23, 23, 23, 23, 12, 2, 13, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 43, 43, 43, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4, 23, 23] 45 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]) total number of confs: 147 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461512010 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512010 Building ZINC000461512011 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461512011 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/394 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461512011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512011 none CS(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 5 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/395 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/395' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461512011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512011 none CS(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 4 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461512011 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 Building ZINC000461512011 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461512011 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 394) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461512011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512011 none CS(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 5, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3] 5 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 395) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000461512011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461512011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000461512011 none CS(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 4 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461512011 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461512011 Building ZINC000732023599 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732023599 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/396 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1) `ZINC000732023599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732023599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023599 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 8, 18, 27, 27, 27, 27, 27, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/397 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1) `ZINC000732023599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732023599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023599 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 17, 25, 25, 25, 25, 25, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 25, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732023599 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 Building ZINC000732023599 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732023599 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 396) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/396: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1) `ZINC000732023599.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732023599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023599 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 1, 5, 6, 8, 8, 8, 8, 8, 8, 8, 18, 27, 27, 27, 27, 27, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 115 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 397) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1) `ZINC000732023599.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732023599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023599 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 8, 8, 17, 25, 25, 25, 25, 25, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 25, 25, 25, 25, 25, 25, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 124 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732023599 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023599 Building ZINC000732023600 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732023600 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/398 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1) `ZINC000732023600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732023600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023600 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 18, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/399 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1) `ZINC000732023600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732023600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023600 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 16, 28, 28, 28, 28, 28, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732023600 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 Building ZINC000732023600 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732023600 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 398) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1) `ZINC000732023600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732023600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023600 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 18, 27, 27, 27, 27, 27, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 27, 27, 27, 27, 27, 27, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 127 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 399) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/399: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1) `ZINC000732023600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732023600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000732023600 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCC[C@@H]2CN2CCCC2=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 8, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 16, 28, 28, 28, 28, 28, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 28, 28, 28, 28, 28, 28, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732023600 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732023600 Building ZINC000461610470 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461610470 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/400 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461610470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461610470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000461610470 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 10, 29, 29, 58, 29, 29, 29, 29, 29, 29] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/401 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461610470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461610470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000461610470 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 10, 29, 29, 58, 29, 29, 29, 29, 29, 29] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461610470 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 Building ZINC000461610470 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461610470 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 400) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461610470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461610470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000461610470 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 10, 29, 29, 58, 29, 29, 29, 29, 29, 29] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 401) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/401: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461610470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461610470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000461610470 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 9, 9, 9, 9, 10, 29, 29, 58, 29, 29, 29, 29, 29, 29] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461610470 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461610470 Building ZINC000461631083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461631083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/402 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21) `ZINC000461631083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461631083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000461631083 none Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 20, 20, 20, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 34, 17] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/403 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21) `ZINC000461631083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461631083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000461631083 none Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 34, 17] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461631083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 Building ZINC000461631083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461631083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 402) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21) `ZINC000461631083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461631083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000461631083 none Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 20, 20, 20, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 34, 17] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 403) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21) `ZINC000461631083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461631083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000461631083 none Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C(C)(C)C)c3)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 34, 17] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461631083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461631083 Building ZINC000461634037 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461634037 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/404 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21) `ZINC000461634037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461634037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000461634037 none Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/405 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21) `ZINC000461634037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461634037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000461634037 none Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461634037 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 Building ZINC000461634037 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461634037 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 404) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/404: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21) `ZINC000461634037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461634037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000461634037 none Cn1c(=O)n(C)c2cc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 405) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21) `ZINC000461634037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461634037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000461634037 none Cn1c(=O)n(C)c2cc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)c(O)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 5, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 40, 20] 100 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461634037 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634037 Building ZINC000461634059 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461634059 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/406 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461634059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461634059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000461634059 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 11, 39, 39, 78, 39, 39, 39, 39, 39, 39] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/407 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461634059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461634059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000461634059 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 11, 39, 39, 78, 39, 39, 39, 39, 39, 39] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461634059 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 Building ZINC000461634059 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461634059 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 406) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461634059.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461634059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000461634059 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 11, 39, 39, 78, 39, 39, 39, 39, 39, 39] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 407) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C) `ZINC000461634059.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461634059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000461634059 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)Nc1cc2c(cc1O)n(C)c(=O)n2C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.am', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6, 6, 6, 6, 11, 39, 39, 78, 39, 39, 39, 39, 39, 39] 100 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461634059 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461634059 Building ZINC000461645026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461645026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/408 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461645026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645026 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 18, 18, 18, 35, 35, 35, 31, 29, 20, 20, 2, 2, 2, 2, 2, 18, 18, 18] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/409 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461645026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645026 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 20, 20, 20, 34, 34, 34, 34, 33, 26, 26, 3, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461645026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 Building ZINC000461645026 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461645026 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 408) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/408: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461645026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645026 none COCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 18, 18, 18, 35, 35, 35, 31, 29, 20, 20, 2, 2, 2, 2, 2, 18, 18, 18] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 409) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/409: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461645026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645026 none COCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 10, 20, 20, 20, 34, 34, 34, 34, 33, 26, 26, 3, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461645026 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645026 Building ZINC000461645129 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461645129 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/410 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461645129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645129 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 20, 20, 20, 34, 34, 34, 34, 33, 26, 26, 3, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/411 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461645129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645129 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 18, 18, 18, 35, 35, 35, 31, 29, 20, 20, 2, 2, 2, 2, 2, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461645129 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 Building ZINC000461645129 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000461645129 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 410) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/410: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000461645129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645129 none COCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 20, 20, 20, 34, 34, 34, 34, 33, 26, 26, 3, 2, 2, 2, 2, 20, 20, 20] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 411) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000461645129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000461645129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC000461645129 none COCC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 17, 7, 2, 7, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 7, 18, 18, 18, 35, 35, 35, 31, 29, 20, 20, 2, 2, 2, 2, 2, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000461645129 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000461645129 Building ZINC000764126158 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000764126158 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/412 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000764126158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126158 none O=C(N1CCN2C(=O)OC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 4, 4, 1, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4] 35 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/413 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000764126158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126158 none O=C(N1CCN2C(=O)OC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 2, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5] 31 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000764126158 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 Building ZINC000764126158 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000764126158 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 412) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126158.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000764126158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126158 none O=C(N1CCN2C(=O)OC[C@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 4, 4, 1, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4] 35 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]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 413) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/413: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126158.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000764126158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126158 none O=C(N1CCN2C(=O)OC[C@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 2, 20, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 5, 5, 2, 2, 5, 5, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 5, 5] 31 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000764126158 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126158 Building ZINC000764126161 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000764126161 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/414 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000764126161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126161 none O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 33 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/415 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000764126161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126161 none O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 1, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 1, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4] 34 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000764126161 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 Building ZINC000764126161 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000764126161 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 414) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/414: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000764126161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126161 none O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 14, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 33 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]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 415) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/415: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000764126161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000764126161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000764126161 none O=C(N1CCN2C(=O)OC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 12, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 1, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 1, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4] 34 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000764126161 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000764126161 Building ZINC000274889902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274889902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/416 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1) `ZINC000274889902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274889902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274889902 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 20, 28, 50, 50, 50, 50, 50, 20, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/417 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1) `ZINC000274889902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274889902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274889902 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 27, 50, 50, 50, 50, 50, 18, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274889902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 Building ZINC000274889902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000274889902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 416) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1) `ZINC000274889902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000274889902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274889902 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 20, 20, 28, 50, 50, 50, 50, 50, 20, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 417) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1) `ZINC000274889902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000274889902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000274889902 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cccc(N2CCOCC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 27, 50, 50, 50, 50, 50, 18, 2, 2, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000274889902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000274889902 Building ZINC000174225902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174225902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/418 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174225902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225902 none O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 11, 11, 11, 11, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/419 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174225902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225902 none O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 9, 9, 9, 9, 17, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 6, 3, 9, 9, 30, 30, 30, 30, 30, 30, 5, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174225902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 Building ZINC000174225902 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174225902 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 418) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174225902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225902 none O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 11, 11, 11, 11, 19, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 33, 33, 33, 33, 33, 33, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 419) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/419: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174225902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225902 none O=C(Nc1ccnn1[C@@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 9, 9, 9, 9, 17, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 6, 3, 9, 9, 30, 30, 30, 30, 30, 30, 5, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174225902 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225902 Building ZINC000174225912 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174225912 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/420 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174225912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225912 none O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 9, 9, 9, 9, 16, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/421 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174225912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225912 none O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 11, 11, 11, 11, 19, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174225912 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 Building ZINC000174225912 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174225912 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 420) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/420: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174225912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225912 none O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 9, 9, 9, 9, 16, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 27, 27, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 421) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000174225912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174225912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000174225912 none O=C(Nc1ccnn1[C@H]1CCS(=O)(=O)C1)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 5, 7, 5, 5, 14, 11, 11, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 3, 11, 11, 11, 11, 19, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174225912 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174225912 Building ZINC000171091207 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171091207 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/422 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1) `ZINC000171091207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171091207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000171091207 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 8, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 28, 28, 28, 28, 28, 28, 9, 8, 9, 9, 9, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 56, 28] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/423 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1) `ZINC000171091207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171091207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000171091207 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 8, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 27, 27, 9, 9, 8, 9, 9, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 54, 27] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171091207 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 Building ZINC000171091207 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171091207 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 422) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1) `ZINC000171091207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171091207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000171091207 none O=C(NCCCNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 8, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 28, 28, 28, 28, 28, 28, 9, 8, 9, 9, 9, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 56, 28] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 423) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/423: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1) `ZINC000171091207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171091207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000171091207 none O=C(NCCCNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)c1cccc(O)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 8, 7, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 27, 27, 27, 27, 27, 27, 9, 9, 8, 9, 9, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 54, 27] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171091207 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171091207 Building ZINC000275111342 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111342 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/424 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111342 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 29, 29, 35, 35, 35, 35, 21, 6, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/425 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111342 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 28, 28, 33, 34, 34, 34, 20, 5, 20, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111342 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 Building ZINC000275111342 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111342 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 424) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111342 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 29, 29, 35, 35, 35, 35, 21, 6, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 425) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111342 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 28, 28, 33, 34, 34, 34, 20, 5, 20, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 34, 34, 34, 34, 34, 34, 34, 34, 34, 20, 20, 3, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111342 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111342 Building ZINC000275111345 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111345 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/426 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111345 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 28, 28, 35, 35, 35, 35, 20, 5, 20, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/427 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111345 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 28, 28, 35, 35, 35, 35, 21, 6, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111345 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 Building ZINC000275111345 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111345 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 426) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111345 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 28, 28, 35, 35, 35, 35, 20, 5, 20, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20, 20, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 427) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111345 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 28, 28, 35, 35, 35, 35, 21, 6, 21, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111345 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111345 Building ZINC000275111346 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111346 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/428 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111346 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 27, 27, 36, 36, 36, 36, 18, 7, 18, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/429 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111346 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 28, 28, 33, 33, 33, 33, 18, 9, 18, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111346 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 Building ZINC000275111346 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111346 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 428) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/428: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111346.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111346 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 27, 27, 36, 36, 36, 36, 18, 7, 18, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 36, 36, 36, 36, 36, 36, 36, 36, 36, 18, 18, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 429) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111346.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111346 none C[C@H]1CCN(C(=O)OC(C)(C)C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 28, 28, 33, 33, 33, 33, 18, 9, 18, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111346 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111346 Building ZINC000275111348 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111348 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/430 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111348 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 28, 28, 34, 34, 34, 34, 17, 7, 17, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 3, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/431 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111348 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 27, 27, 35, 35, 35, 35, 17, 6, 17, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 2, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111348 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 Building ZINC000275111348 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275111348 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 430) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111348 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 28, 28, 34, 34, 34, 34, 17, 7, 17, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 3, 8, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 431) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/431: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000275111348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275111348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000275111348 none C[C@@H]1CCN(C(=O)OC(C)(C)C)C[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 27, 27, 35, 35, 35, 35, 17, 6, 17, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 35, 35, 17, 17, 2, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275111348 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275111348 Building ZINC000275138805 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138805 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/432 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138805 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 13, 13, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 3, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/433 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138805 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 15, 21, 21, 21, 21, 5, 5, 5, 5, 5, 6, 6, 17, 17, 17, 17, 17, 6, 2, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138805 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 Building ZINC000275138805 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138805 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 432) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/432: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138805 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 13, 13, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 17, 7, 3, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 433) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138805 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 15, 21, 21, 21, 21, 5, 5, 5, 5, 5, 6, 6, 17, 17, 17, 17, 17, 6, 2, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138805 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138805 Building ZINC000275138807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/434 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138807 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 22, 23, 23, 23, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 6, 2, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/435 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138807 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 15, 15, 19, 19, 19, 19, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 14, 14, 6, 3, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 Building ZINC000275138807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 434) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138807 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 22, 23, 23, 23, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 6, 2, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 435) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1) `ZINC000275138807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138807 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 15, 15, 19, 19, 19, 19, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 14, 14, 6, 3, 10, 10, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138807 Building ZINC000275138809 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138809 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/436 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138809 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 13, 13, 19, 19, 19, 19, 6, 6, 6, 6, 6, 7, 7, 15, 15, 15, 15, 15, 7, 2, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/437 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138809 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 13, 13, 17, 18, 18, 18, 7, 7, 7, 7, 7, 8, 8, 17, 17, 17, 17, 17, 8, 3, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138809 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 Building ZINC000275138809 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138809 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 436) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/436: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138809 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 13, 13, 19, 19, 19, 19, 6, 6, 6, 6, 6, 7, 7, 15, 15, 15, 15, 15, 7, 2, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 437) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138809 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 13, 13, 17, 18, 18, 18, 7, 7, 7, 7, 7, 8, 8, 17, 17, 17, 17, 17, 8, 3, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 7, 7, 7, 7, 7, 8] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138809 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138809 Building ZINC000275138812 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138812 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/438 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138812 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 15, 15, 20, 20, 20, 20, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 14, 14, 6, 3, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/439 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138812 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 23, 24, 24, 24, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 6, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138812 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 Building ZINC000275138812 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275138812 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 438) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275138812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138812 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 10, 10, 10, 10, 15, 15, 20, 20, 20, 20, 10, 10, 10, 10, 10, 6, 6, 14, 14, 14, 14, 14, 6, 3, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 439) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/439: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1) `ZINC000275138812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275138812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000275138812 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CN(C(=O)OC(C)(C)C)CC[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 16, 16, 23, 24, 24, 24, 9, 9, 9, 9, 9, 6, 6, 13, 13, 13, 13, 13, 6, 2, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 9, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275138812 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275138812 Building ZINC000732100216 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732100216 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/440 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1) `ZINC000732100216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732100216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100216 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 11, 21, 21, 34, 35, 35, 34, 35, 35, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 8, 11, 11, 34, 34, 35, 35, 35, 35, 35, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/441 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1) `ZINC000732100216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732100216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100216 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 9, 20, 20, 36, 36, 36, 36, 36, 36, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 6, 6, 9, 9, 36, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732100216 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 Building ZINC000732100216 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732100216 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 440) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/440: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1) `ZINC000732100216.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732100216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100216 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 11, 21, 21, 34, 35, 35, 34, 35, 35, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 8, 8, 11, 11, 34, 34, 35, 35, 35, 35, 35, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 441) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/441: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1) `ZINC000732100216.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732100216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100216 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 9, 20, 20, 36, 36, 36, 36, 36, 36, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 6, 6, 9, 9, 36, 36, 36, 36, 36, 36, 36, 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732100216 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100216 Building ZINC000732100217 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732100217 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/442 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1) `ZINC000732100217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732100217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100217 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 9, 20, 20, 35, 35, 35, 35, 35, 35, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 6, 6, 9, 9, 35, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/443 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1) `ZINC000732100217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732100217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100217 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 11, 21, 21, 34, 35, 35, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 8, 8, 11, 11, 34, 34, 35, 35, 35, 35, 35, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732100217 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 Building ZINC000732100217 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000732100217 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 442) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1) `ZINC000732100217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000732100217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100217 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 9, 20, 20, 35, 35, 35, 35, 35, 35, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 2, 6, 6, 9, 9, 35, 35, 35, 35, 35, 35, 35, 5] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 443) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1) `ZINC000732100217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000732100217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000732100217 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCC[S@](=O)Cc2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o', 'O.2', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 11, 21, 21, 34, 35, 35, 35, 35, 35, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 8, 8, 11, 11, 34, 34, 35, 35, 35, 35, 35, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000732100217 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000732100217 Building ZINC000174365370 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174365370 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/444 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174365370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365370 none COC(=O)C[C@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 14, 26, 14, 5, 14, 14, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 5, 26, 26, 26, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/445 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174365370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365370 none COC(=O)C[C@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 18, 26, 17, 7, 17, 17, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 26, 26, 26, 18, 18, 17, 17, 17, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174365370 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 Building ZINC000174365370 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174365370 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 444) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/444: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365370.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174365370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365370 none COC(=O)C[C@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 14, 26, 14, 5, 14, 14, 5, 5, 5, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 5, 5, 26, 26, 26, 14, 14, 14, 14, 14, 5, 5, 5, 5, 2, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 445) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/445: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365370.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174365370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365370 none COC(=O)C[C@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 18, 26, 17, 7, 17, 17, 7, 7, 7, 4, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 26, 26, 26, 18, 18, 17, 17, 17, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 94 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174365370 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365370 Building ZINC000174365387 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174365387 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/446 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174365387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365387 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 17, 26, 14, 6, 14, 14, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 6, 6, 26, 26, 26, 17, 17, 14, 14, 14, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/447 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174365387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365387 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 27, 15, 4, 15, 15, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 4, 4, 27, 27, 27, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174365387 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 Building ZINC000174365387 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174365387 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 446) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174365387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365387 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 17, 26, 14, 6, 14, 14, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 6, 6, 26, 26, 26, 17, 17, 14, 14, 14, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 116 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 447) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000174365387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174365387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000174365387 none COC(=O)C[C@@H](C)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 15, 27, 15, 4, 15, 15, 4, 4, 4, 2, 1, 4, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 4, 4, 27, 27, 27, 15, 15, 15, 15, 15, 4, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 118 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174365387 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174365387 Building ZINC000174412962 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174412962 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/448 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174412962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412962 none C[C@@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 7, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/449 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174412962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412962 none C[C@@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174412962 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 Building ZINC000174412962 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174412962 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 448) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/448: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412962.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174412962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412962 none C[C@@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 7, 7, 7, 7, 3, 2, 5, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 7, 7, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 2, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 449) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412962.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174412962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412962 none C[C@@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 9, 9, 28, 28, 28, 28, 28, 28, 9, 9, 9, 9, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174412962 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412962 Building ZINC000174412977 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174412977 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/450 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174412977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412977 none C[C@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 25, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 9, 9, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/451 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/451' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174412977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412977 none C[C@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 25, 8, 8, 8, 8, 3, 2, 5, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 8, 8, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174412977 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 Building ZINC000174412977 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174412977 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 450) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174412977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412977 none C[C@H]1CN=C(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 25, 9, 9, 9, 9, 4, 2, 7, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 9, 9, 26, 26, 26, 26, 26, 26, 9, 9, 9, 9, 3, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 451) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1) `ZINC000174412977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174412977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000174412977 none C[C@H]1CN=C(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 25, 8, 8, 8, 8, 3, 2, 5, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 8, 8, 26, 26, 26, 26, 26, 26, 8, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174412977 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174412977 Building ZINC000171300246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171300246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/452 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccn1)C(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171300246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171300246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171300246 none CN(CCc1ccccn1)C(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 27, 27, 27, 27, 27, 27, 27, 11, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/453 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccn1)C(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171300246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171300246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171300246 none CN(CCc1ccccn1)C(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 28, 28, 28, 28, 28, 28, 28, 11, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171300246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 Building ZINC000171300246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171300246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 452) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/452: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccn1)C(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171300246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171300246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171300246 none CN(CCc1ccccn1)C(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 17, 23, 27, 27, 27, 27, 27, 27, 27, 11, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 453) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/453: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCc1ccccn1)C(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2) `ZINC000171300246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171300246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000171300246 none CN(CCc1ccccn1)C(=O)CNC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 24, 28, 28, 28, 28, 28, 28, 28, 11, 17, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 28, 28, 28, 28, 28, 28, 28, 28, 11, 11, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171300246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171300246 Building ZINC000462379275 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462379275 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/454 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2) `ZINC000462379275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462379275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000462379275 none Cn1nc2c(c1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 28, 28, 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, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/455 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1CNC(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2) `ZINC000462379275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462379275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000462379275 none Cn1nc2c(c1CNC(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 27, 27, 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, 47]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462379275 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 Building ZINC000462379275 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462379275 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 454) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/454: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2) `ZINC000462379275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462379275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000462379275 none Cn1nc2c(c1CNC(=O)[C@@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 12, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6, 28, 28, 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, 47]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 455) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nc2c(c1CNC(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2) `ZINC000462379275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462379275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000462379275 none Cn1nc2c(c1CNC(=O)[C@]([O-])([SiH3])c1cnn(c3ccccc3)c1)CCCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 11, 11, 2, 6, 6, 6, 6, 6, 6, 6, 27, 27, 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, 47]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462379275 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462379275 Building ZINC000174522389 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174522389 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/456 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)COc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000174522389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174522389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000174522389 none NC(=O)COc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 33, 28, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 33, 33, 28, 28, 14, 14, 14, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14] 50 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/457 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)COc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000174522389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174522389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000174522389 none NC(=O)COc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 32, 32, 28, 28, 14, 14, 14, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14] 50 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174522389 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 Building ZINC000174522389 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174522389 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 456) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)COc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000174522389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174522389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000174522389 none NC(=O)COc1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 28, 33, 28, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 33, 33, 28, 28, 14, 14, 14, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14] 50 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 457) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/457: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)COc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1) `ZINC000174522389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174522389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000174522389 none NC(=O)COc1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 32, 28, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 14, 32, 32, 28, 28, 14, 14, 14, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14] 50 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000174522389 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000174522389 Building ZINC000275440252 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440252 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/458 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440252 none CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 15, 15, 15, 15, 11, 7, 1, 7, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 38, 38, 38, 15, 15, 15, 26, 26, 26, 26, 26, 15, 15, 7, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/459 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440252 none CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 13, 13, 13, 8, 6, 1, 6, 1, 1, 1, 5, 5, 3, 5, 5, 5, 5, 13, 31, 31, 31, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440252 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 Building ZINC000275440252 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440252 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 458) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/458: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440252 none CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 15, 15, 15, 15, 11, 7, 1, 7, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 38, 38, 38, 15, 15, 15, 26, 26, 26, 26, 26, 15, 15, 7, 4, 4, 4, 4, 4, 4, 4, 38, 38, 38, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 459) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440252 none CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 13, 13, 13, 8, 6, 1, 6, 1, 1, 1, 5, 5, 3, 5, 5, 5, 5, 13, 31, 31, 31, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440252 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440252 Building ZINC000275440256 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440256 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/460 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440256 none CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 16, 16, 16, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 39, 39, 39, 16, 16, 16, 33, 33, 33, 33, 33, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 39, 39, 39, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/461 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440256 none CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 16, 16, 16, 16, 12, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 37, 37, 37, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440256 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 Building ZINC000275440256 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440256 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 460) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440256.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440256 none CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 16, 16, 16, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 39, 39, 39, 16, 16, 16, 33, 33, 33, 33, 33, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 39, 39, 39, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 163 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 461) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440256.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440256 none CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 16, 16, 16, 16, 12, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 37, 37, 37, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440256 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440256 Building ZINC000275440260 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440260 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/462 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440260 none CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 16, 16, 16, 16, 12, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 37, 37, 37, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/463 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440260 none CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 16, 16, 16, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 40, 40, 40, 16, 16, 16, 32, 32, 32, 32, 32, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440260 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 Building ZINC000275440260 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440260 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 462) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440260 none CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 16, 16, 16, 16, 12, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 37, 37, 37, 16, 16, 16, 29, 29, 29, 29, 29, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 37, 37, 37, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 463) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/463: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440260 none CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 16, 16, 16, 16, 11, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 16, 40, 40, 40, 16, 16, 16, 32, 32, 32, 32, 32, 16, 16, 6, 3, 3, 3, 3, 3, 3, 3, 40, 40, 40, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440260 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440260 Building ZINC000275440264 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440264 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/464 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440264 none CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 13, 13, 13, 8, 6, 1, 6, 1, 1, 1, 5, 5, 3, 5, 5, 5, 5, 13, 31, 31, 31, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/465 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440264 none CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 15, 15, 15, 11, 7, 1, 7, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 37, 37, 37, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 7, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440264 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 Building ZINC000275440264 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275440264 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 464) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275440264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440264 none CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 13, 13, 13, 13, 8, 6, 1, 6, 1, 1, 1, 5, 5, 3, 5, 5, 5, 5, 13, 31, 31, 31, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 6, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 465) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C) `ZINC000275440264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275440264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275440264 none CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 15, 15, 15, 15, 11, 7, 1, 7, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 15, 37, 37, 37, 15, 15, 15, 27, 27, 27, 27, 27, 15, 15, 7, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275440264 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275440264 Building ZINC000462592614 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462592614 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/466 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000462592614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462592614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000462592614 none O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 22, 22, 22, 29, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/467 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000462592614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462592614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000462592614 none O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 22, 22, 22, 27, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462592614 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 Building ZINC000462592614 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462592614 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 466) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000462592614.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462592614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000462592614 none O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 22, 22, 22, 29, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 467) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000462592614.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462592614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000462592614 none O=C(NCc1cnc(N2CCOCC2)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 1, 8, 5, 5, 12, 5, 5, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 22, 22, 22, 27, 50, 50, 50, 50, 50, 22, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462592614 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462592614 Building ZINC000847269802 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847269802 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/468 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847269802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269802 none O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 32, 32, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 15, 15, 32, 32, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/469 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847269802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269802 none O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 22, 33, 33, 33, 33, 50, 50, 33, 33, 33, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 13, 13, 33, 33, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847269802 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 Building ZINC000847269802 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847269802 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 468) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847269802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269802 none O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 32, 32, 32, 32, 50, 50, 32, 32, 32, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 15, 15, 32, 32, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 469) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847269802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269802 none O=C(NC[C@@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 22, 33, 33, 33, 33, 50, 50, 33, 33, 33, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 13, 13, 33, 33, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847269802 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269802 Building ZINC000847269803 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847269803 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/470 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847269803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269803 none O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 25, 37, 37, 37, 37, 50, 50, 37, 37, 37, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/471 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847269803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269803 none O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 26, 35, 35, 35, 35, 50, 50, 35, 35, 35, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 16, 16, 35, 35, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847269803 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 Building ZINC000847269803 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847269803 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 470) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269803.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847269803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269803 none O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 25, 37, 37, 37, 37, 50, 50, 37, 37, 37, 1, 1, 1, 3, 3, 1, 1, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 471) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000847269803.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847269803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000847269803 none O=C(NC[C@H]1CN(C2CC2)C(=O)O1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 26, 35, 35, 35, 35, 50, 50, 35, 35, 35, 1, 1, 1, 3, 3, 1, 3, 3, 3, 4, 16, 16, 35, 35, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847269803 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847269803 Building ZINC000462762436 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462762436 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/472 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462762436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762436 none COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 28, 13, 13, 13, 13, 13, 13, 13, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 45, 45, 28, 28, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 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]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/473 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462762436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762436 none COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 31, 12, 12, 12, 12, 12, 12, 12, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 44, 44, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3] 50 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]) total number of confs: 205 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462762436 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 Building ZINC000462762436 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462762436 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 472) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/472: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762436.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462762436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762436 none COCC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 28, 13, 13, 13, 13, 13, 13, 13, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 45, 45, 28, 28, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 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]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 473) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/473: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762436.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462762436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762436 none COCC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 31, 12, 12, 12, 12, 12, 12, 12, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 44, 44, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3] 50 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]) total number of confs: 205 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462762436 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762436 Building ZINC000462762438 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462762438 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/474 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462762438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762438 none COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 31, 12, 12, 12, 12, 12, 12, 12, 9, 2, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 44, 44, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3] 50 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]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/475 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462762438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762438 none COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 29, 13, 13, 13, 13, 13, 13, 13, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 45, 45, 29, 29, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 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]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462762438 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 Building ZINC000462762438 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000462762438 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 474) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762438.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000462762438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762438 none COCC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 31, 12, 12, 12, 12, 12, 12, 12, 9, 2, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 50, 50, 50, 44, 44, 31, 31, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3] 50 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]) total number of confs: 208 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 475) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000462762438.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000462762438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000462762438 none COCC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 29, 13, 13, 13, 13, 13, 13, 13, 11, 2, 11, 1, 1, 1, 3, 3, 1, 1, 3, 3, 50, 50, 50, 45, 45, 29, 29, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 50 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]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000462762438 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000462762438 Building ZINC000275575808 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575808 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/476 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575808 none CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 7, 7, 7, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 19, 7, 7, 7, 23, 23, 23, 23, 23, 7, 7, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/477 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575808 none CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 10, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 26, 26, 26, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575808 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 Building ZINC000275575808 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575808 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 476) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/476: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575808 none CCO[C@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 7, 7, 7, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 19, 7, 7, 7, 23, 23, 23, 23, 23, 7, 7, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 106 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 477) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575808 none CCO[C@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 10, 10, 10, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 26, 26, 26, 10, 10, 10, 21, 21, 21, 21, 21, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 26, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575808 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575808 Building ZINC000275575813 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575813 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/478 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575813 none CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 8, 8, 8, 18, 18, 18, 18, 18, 8, 8, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 8, 8, 8, 8, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/479 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575813 none CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575813 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 Building ZINC000275575813 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575813 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 478) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575813 none CCO[C@@H]1C[C@@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 8, 8, 8, 8, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 8, 23, 23, 23, 8, 8, 8, 18, 18, 18, 18, 18, 8, 8, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 8, 8, 8, 8, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 84 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 479) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575813 none CCO[C@@H]1C[C@@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 9, 16, 16, 16, 16, 16, 9, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 83 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575813 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575813 Building ZINC000275575817 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575817 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/480 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575817 none CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/481 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575817 none CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 9, 19, 19, 19, 19, 19, 9, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575817 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 Building ZINC000275575817 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575817 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 480) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575817 none CCO[C@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 10, 10, 10, 10, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 10, 17, 17, 17, 17, 17, 10, 10, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 481) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/481: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575817 none CCO[C@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 9, 9, 9, 9, 7, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 21, 21, 21, 9, 9, 9, 19, 19, 19, 19, 19, 9, 9, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 21, 21, 21, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575817 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575817 Building ZINC000275575822 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575822 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/482 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575822 none CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/483 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575822 none CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 7, 7, 7, 7, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 19, 7, 7, 7, 21, 21, 21, 21, 21, 7, 7, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575822 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 Building ZINC000275575822 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000275575822 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 482) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575822.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000275575822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575822 none CCO[C@@H]1C[C@](NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 10, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 10, 22, 22, 22, 10, 10, 10, 19, 19, 19, 19, 19, 10, 10, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 22, 22, 22, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 483) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C) `ZINC000275575822.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000275575822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000275575822 none CCO[C@@H]1C[C@](NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)(C(=O)OC)C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 7, 7, 7, 7, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 19, 19, 19, 7, 7, 7, 21, 21, 21, 21, 21, 7, 7, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 19, 19, 19, 7, 7, 7, 7, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000275575822 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000275575822 Building ZINC000463012692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000463012692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/484 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/485 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/486 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/486' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/487 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/487' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000463012692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 Building ZINC000463012692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000463012692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 484) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 485) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 486) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 487) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000463012692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 Building ZINC000463012692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000463012692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 484) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 485) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 486) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 487) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000463012692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 Building ZINC000463012692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000463012692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 484) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 485) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 486) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 8, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 9, 28, 28, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 487) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000463012692.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000463012692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000463012692 none O=C(Nc1cccc(CN2CCNC(=O)C2)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 8, 1, 11, 5, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 9, 9, 2, 9, 9, 47, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 9, 9, 2, 29, 29, 50, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2] 50 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000463012692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000463012692 Building ZINC001525896525 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525896525 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/488 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/488' -> `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)NCc1c(F)cccc1n1cccn1) `ZINC001525896525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525896525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001525896525 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 27, 38, 38, 38, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 38, 38, 42, 42, 42] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/489 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/489' -> `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)NCc1c(F)cccc1n1cccn1) `ZINC001525896525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525896525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001525896525 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 21, 38, 38, 38, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 38, 38, 42, 42, 42] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525896525 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 Building ZINC001525896525 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525896525 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 488) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/488: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1) `ZINC001525896525.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525896525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001525896525 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 27, 38, 38, 38, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 38, 38, 42, 42, 42] 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]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 489) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/489: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1) `ZINC001525896525.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525896525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001525896525 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1c(F)cccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 15, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 20, 38, 38, 38, 21, 38, 38, 38, 42, 42, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 20, 20, 38, 38, 38, 42, 42, 42] 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]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525896525 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525896525 Building ZINC001350279954 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350279954 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/490 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350279954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350279954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001350279954 none Cn1ccnc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 18, 18, 18, 18, 4, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 48, 48, 48, 48, 48, 54, 18, 18, 3, 1, 3, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/491 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1C1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350279954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350279954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001350279954 none Cn1ccnc1C1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 49, 49, 49, 49, 49, 69, 23, 23, 3, 1, 3, 23, 23] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350279954 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 Building ZINC001350279954 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350279954 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 490) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350279954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350279954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001350279954 none Cn1ccnc1C1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 18, 18, 18, 18, 4, 1, 6, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 18, 48, 48, 48, 48, 48, 54, 18, 18, 3, 1, 3, 18, 18] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 491) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccnc1C1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350279954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350279954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001350279954 none Cn1ccnc1C1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 23, 23, 23, 23, 4, 1, 8, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 23, 49, 49, 49, 49, 49, 69, 23, 23, 3, 1, 3, 23, 23] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 151 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350279954 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350279954 Building ZINC001287273047 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287273047 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/492 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287273047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273047 none C[C@@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 28, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 44, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/493 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287273047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273047 none C[C@@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 25, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 38, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287273047 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 Building ZINC001287273047 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287273047 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 492) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/492: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273047.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287273047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273047 none C[C@@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 28, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 44, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 212 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 493) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/493: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273047.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287273047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273047 none C[C@@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 25, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 38, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287273047 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273047 Building ZINC001287273048 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287273048 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/494 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287273048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273048 none C[C@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 37, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/495 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287273048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273048 none C[C@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287273048 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 Building ZINC001287273048 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287273048 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 494) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/494: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273048.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287273048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273048 none C[C@H](CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 37, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 495) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/495: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287273048.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287273048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001287273048 none C[C@H](CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 28, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 15, 15, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287273048 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287273048 Building ZINC001525962930 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525962930 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/496 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1) `ZINC001525962930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525962930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001525962930 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 14, 5, 11, 11, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 5, 12, 12, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 23, 23, 23, 12, 19, 19, 19, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/497 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1) `ZINC001525962930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525962930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001525962930 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 14, 5, 11, 11, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 25, 25, 25, 12, 19, 19, 19, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525962930 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 Building ZINC001525962930 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001525962930 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 496) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1) `ZINC001525962930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001525962930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001525962930 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 14, 5, 11, 11, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 7, 5, 12, 12, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 23, 23, 23, 12, 19, 19, 19, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 497) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1) `ZINC001525962930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001525962930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 47 natoms 46 natoms 45 natoms 44 names: ZINC001525962930 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c(S(C)(=O)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 14, 5, 11, 11, 1, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 25, 25, 25, 12, 19, 19, 19, 12, 12, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 12] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 96 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001525962930 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001525962930 Building ZINC000276150519 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276150519 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/498 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n1) `ZINC000276150519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276150519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000276150519 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 28, 44, 28, 28, 28, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 44, 44, 44, 44, 44, 28, 12, 12, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/499 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n1) `ZINC000276150519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276150519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000276150519 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 27, 27, 27, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 27, 43, 43, 43, 43, 43, 27, 12, 12, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276150519 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 Building ZINC000276150519 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276150519 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 498) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n1) `ZINC000276150519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276150519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000276150519 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 28, 44, 28, 28, 28, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 44, 44, 44, 44, 44, 28, 12, 12, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 499) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n1) `ZINC000276150519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276150519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000276150519 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 27, 27, 27, 12, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 27, 43, 43, 43, 43, 43, 27, 12, 12, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276150519 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150519 Building ZINC000276150521 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276150521 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/500 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n1) `ZINC000276150521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276150521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000276150521 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 22, 38, 22, 22, 22, 14, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 22, 50, 50, 50, 50, 50, 22, 14, 14, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/501 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n1) `ZINC000276150521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276150521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000276150521 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 24, 39, 24, 24, 24, 16, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 24, 50, 50, 50, 50, 50, 24, 16, 16, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276150521 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 Building ZINC000276150521 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276150521 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 500) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/500: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n1) `ZINC000276150521.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276150521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000276150521 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 38, 22, 38, 22, 22, 22, 14, 12, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 22, 50, 50, 50, 50, 50, 22, 14, 14, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 501) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/501: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n1) `ZINC000276150521.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276150521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000276150521 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2OC)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 24, 39, 24, 24, 24, 16, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 24, 50, 50, 50, 50, 50, 24, 16, 16, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276150521 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276150521 Building ZINC001128965039 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001128965039 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/502 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001128965039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001128965039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001128965039 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 26, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/503 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/503' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001128965039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001128965039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001128965039 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 17, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001128965039 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 Building ZINC001128965039 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001128965039 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 502) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001128965039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001128965039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001128965039 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 15, 26, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 5, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 503) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1) `ZINC001128965039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001128965039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001128965039 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CCS(=O)(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.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', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 17, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 4, 4, 4, 4, 4, 4, 4, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001128965039 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001128965039 Building ZINC000276179403 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276179403 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/504 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000276179403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276179403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000276179403 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.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.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 15, 4, 15, 4, 4, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 18, 5, 4, 32, 32, 32, 32, 32, 4, 3, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/505 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000276179403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276179403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000276179403 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.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.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 15, 4, 15, 4, 4, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 17, 5, 4, 33, 33, 33, 33, 33, 4, 3, 3, 3, 3, 3, 5, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276179403 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 Building ZINC000276179403 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000276179403 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 504) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/504: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000276179403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000276179403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000276179403 none CCOC(=O)c1csc(CCNC(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.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.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 15, 4, 15, 4, 4, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 18, 5, 4, 32, 32, 32, 32, 32, 4, 3, 3, 3, 3, 3, 5, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 505) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/505: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1) `ZINC000276179403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000276179403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000276179403 none CCOC(=O)c1csc(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.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.3', '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, 12, 1, 11, 1, 1, 14, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 15, 4, 15, 4, 4, 4, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 17, 5, 4, 33, 33, 33, 33, 33, 4, 3, 3, 3, 3, 3, 5, 17, 17, 17, 17, 17, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000276179403 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000276179403 Building ZINC000628921257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628921257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/506 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/507 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/508 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/508' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/509 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/509' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628921257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 Building ZINC000628921257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628921257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 506) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 507) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 508) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 509) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628921257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 Building ZINC000628921257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628921257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 506) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 507) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 508) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 509) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628921257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 Building ZINC000628921257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000628921257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 506) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/506: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 507) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/507: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 508) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/508: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 18, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 509) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/509: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C) `ZINC000628921257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000628921257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000628921257 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1COCCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 17, 36, 36, 36, 36, 36, 36, 36, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 16, 16, 36, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 136 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000628921257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000628921257 Building ZINC001350349443 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350349443 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/510 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350349443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350349443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001350349443 none Cn1nccc1C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 9, 9, 25, 25, 25, 25, 25, 27, 9, 9, 9, 9, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9] 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, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/511 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/511' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350349443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350349443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001350349443 none Cn1nccc1C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 1, 5, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 10, 10, 25, 25, 25, 25, 25, 30, 10, 10, 10, 10, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 10, 10, 10, 10] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350349443 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 Building ZINC001350349443 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350349443 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 510) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350349443.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350349443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001350349443 none Cn1nccc1C1(O)CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [25, 25, 25, 25, 25, 9, 9, 9, 9, 9, 5, 2, 5, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 4, 9, 9, 25, 25, 25, 25, 25, 27, 9, 9, 9, 9, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 9, 9, 9, 9] 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, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 511) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1nccc1C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350349443.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350349443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001350349443 none Cn1nccc1C1(O)CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [25, 25, 25, 25, 25, 10, 10, 10, 10, 10, 7, 1, 5, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 10, 10, 25, 25, 25, 25, 25, 30, 10, 10, 10, 10, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 10, 10, 10, 10] 150 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 93 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350349443 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350349443 Building ZINC000560499861 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560499861 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/512 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/512' -> `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)NCc1cnc(C)nc1N) `ZINC000560499861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560499861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000560499861 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N NO_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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 16, 41, 41, 16, 41, 41, 41, 41, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 16, 16, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/513 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/513' -> `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)NCc1cnc(C)nc1N) `ZINC000560499861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560499861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000560499861 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N NO_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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 41, 41, 14, 41, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560499861 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 Building ZINC000560499861 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560499861 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 512) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N) `ZINC000560499861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560499861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000560499861 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N NO_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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 3, 3, 3, 16, 41, 41, 16, 41, 41, 41, 41, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 16, 16, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 513) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/513: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N) `ZINC000560499861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560499861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000560499861 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cnc(C)nc1N NO_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.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 41, 41, 14, 41, 41, 41, 41, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 14, 14, 41, 41, 41, 41, 41, 41] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560499861 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560499861 Building ZINC001350366066 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350366066 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/514 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2cnnn2C)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350366066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350366066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350366066 none COC1(c2cnnn2C)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [30, 14, 14, 14, 43, 43, 43, 43, 43, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 30, 30, 30, 43, 43, 43, 43, 14, 14, 3, 1, 3, 14, 14] 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]) total number of confs: 99 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/515 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/515' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2cnnn2C)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350366066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350366066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350366066 none COC1(c2cnnn2C)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [27, 14, 14, 14, 42, 42, 42, 42, 42, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 27, 27, 27, 42, 42, 42, 42, 14, 14, 3, 3, 3, 14, 14] 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]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350366066 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 Building ZINC001350366066 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350366066 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 514) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/514: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2cnnn2C)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350366066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350366066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350366066 none COC1(c2cnnn2C)CN(C(=O)[C@@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [30, 14, 14, 14, 43, 43, 43, 43, 43, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 1, 3, 3, 3, 14, 30, 30, 30, 43, 43, 43, 43, 14, 14, 3, 1, 3, 14, 14] 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]) total number of confs: 99 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 515) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/515: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(c2cnnn2C)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1) `ZINC001350366066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350366066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350366066 none COC1(c2cnnn2C)CN(C(=O)[C@]([O-])([SiH3])c2cc(Cl)cc(Cl)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 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: [27, 14, 14, 14, 42, 42, 42, 42, 42, 14, 2, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 27, 27, 27, 42, 42, 42, 42, 14, 14, 3, 3, 3, 14, 14] 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]) total number of confs: 84 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350366066 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350366066 Building ZINC001287365364 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287365364 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/516 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/516' -> `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)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1) `ZINC001287365364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287365364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001287365364 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 157 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/517 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/517' -> `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)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1) `ZINC001287365364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287365364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001287365364 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287365364 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 Building ZINC001287365364 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287365364 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 516) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/516: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1) `ZINC001287365364.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287365364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001287365364 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 157 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 517) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/517: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1) `ZINC001287365364.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287365364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001287365364 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CCN(C(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [2, 35, 4, 5, 6, 7, 8, 9, 42, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 153 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287365364 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287365364 Building ZINC001287394067 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287394067 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/518 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287394067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287394067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287394067 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 32, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 48, 48, 39, 39, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/519 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287394067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287394067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287394067 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 33, 23, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 44, 44, 38, 38, 23, 23, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 195 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287394067 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 Building ZINC001287394067 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287394067 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 518) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287394067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287394067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287394067 none CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 32, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 48, 48, 39, 39, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 214 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 519) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287394067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287394067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287394067 none CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 33, 23, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 44, 44, 38, 38, 23, 23, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 195 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287394067 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394067 Building ZINC001287394862 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287394862 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/520 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287394862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287394862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287394862 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 42, 45, 42, 42, 36, 28, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 36, 36, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 55, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/521 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287394862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287394862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287394862 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 43, 49, 43, 43, 34, 25, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 34, 34, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 55, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287394862 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 Building ZINC001287394862 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287394862 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 520) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/520: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287394862.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287394862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287394862 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 42, 45, 42, 42, 36, 28, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 36, 36, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 55, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 521) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/521: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287394862.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287394862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287394862 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 49, 50, 43, 49, 43, 43, 34, 25, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 43, 43, 34, 34, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 56, 54, 55, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287394862 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287394862 Building ZINC001287395030 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287395030 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/522 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001287395030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287395030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287395030 none CN(CCOCCNC(=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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 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, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 35, 27, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 40, 40, 35, 35, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/523 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001287395030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287395030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287395030 none CN(CCOCCNC(=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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 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, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 33, 24, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 39, 39, 33, 33, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287395030 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 Building ZINC001287395030 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287395030 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 522) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/522: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001287395030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287395030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287395030 none CN(CCOCCNC(=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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 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, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 35, 27, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 40, 40, 35, 35, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 523) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCOCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001287395030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287395030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287395030 none CN(CCOCCNC(=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', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 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, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 33, 24, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 39, 39, 33, 33, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287395030 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287395030 Building ZINC000464253095 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464253095 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/524 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)CC2)cn1) `ZINC000464253095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464253095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000464253095 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 2, 4, 7, 9, 9, 9, 9, 14, 14, 22, 36, 36, 36, 36, 36, 36, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 22, 22, 36, 36, 36, 36, 9, 9, 9, 9, 2] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/525 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)CC2)cn1) `ZINC000464253095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464253095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000464253095 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 2, 4, 6, 8, 8, 8, 8, 15, 15, 24, 36, 36, 36, 36, 36, 36, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 24, 24, 36, 36, 36, 36, 8, 8, 8, 8, 2] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464253095 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 Building ZINC000464253095 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464253095 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 524) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)CC2)cn1) `ZINC000464253095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464253095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000464253095 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 2, 4, 7, 9, 9, 9, 9, 14, 14, 22, 36, 36, 36, 36, 36, 36, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 22, 22, 36, 36, 36, 36, 9, 9, 9, 9, 2] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 525) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/525: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)CC2)cn1) `ZINC000464253095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464253095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000464253095 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C(=O)Cc3cccc(Cl)c3)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', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 16, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 2, 4, 6, 8, 8, 8, 8, 15, 15, 24, 36, 36, 36, 36, 36, 36, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 24, 24, 36, 36, 36, 36, 8, 8, 8, 8, 2] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464253095 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464253095 Building ZINC001526123585 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526123585 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/526 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br) `ZINC001526123585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526123585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526123585 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/527 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br) `ZINC001526123585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526123585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526123585 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526123585 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 Building ZINC001526123585 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526123585 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 526) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/526: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br) `ZINC001526123585.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526123585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526123585 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 527) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/527: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br) `ZINC001526123585.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526123585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001526123585 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1nn(C)cc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 8, 5, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 19, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526123585 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526123585 Building ZINC001287452170 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001287452170 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/528 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/529 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/530 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/530' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/531 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/531' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287452170 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 Building ZINC001287452170 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001287452170 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 528) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 529) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 530) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 531) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287452170 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 Building ZINC001287452170 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001287452170 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 528) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 529) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 530) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 531) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287452170 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 Building ZINC001287452170 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001287452170 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 528) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/528: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 529) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/529: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 40, 40, 40, 22, 40, 22, 22, 10, 8, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 40, 40, 40, 40, 42, 42, 42, 42, 42, 22, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 530) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 531) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C) `ZINC001287452170.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001287452170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001287452170 none CC[C@@H]1[C@@H](C(=O)NCC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(C)C)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 44, 44, 24, 44, 24, 24, 11, 10, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 12, 12, 44, 44, 44, 44, 48, 48, 48, 48, 48, 24, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 44, 44, 44, 44, 44, 44, 44] 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287452170 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287452170 Building ZINC000560791130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560791130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/532 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1) `ZINC000560791130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560791130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000560791130 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 17, 1, 8, 1, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 6, 6, 14, 14, 7, 7, 22, 22, 22, 22, 22, 7, 4, 6, 6, 6, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/533 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1) `ZINC000560791130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560791130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000560791130 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 17, 1, 8, 1, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 16, 16, 7, 9, 16, 16, 7, 7, 22, 22, 22, 22, 22, 7, 4, 7, 7, 7, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560791130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 Building ZINC000560791130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560791130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 532) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/532: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1) `ZINC000560791130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560791130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000560791130 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 17, 1, 8, 1, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 14, 14, 6, 6, 14, 14, 7, 7, 22, 22, 22, 22, 22, 7, 4, 6, 6, 6, 14, 14, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 533) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1) `ZINC000560791130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560791130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 38 natoms 37 natoms 36 natoms 35 names: ZINC000560791130 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ncc(Br)cn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 1, 17, 1, 8, 1, 8, 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, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 16, 16, 7, 9, 16, 16, 7, 7, 22, 22, 22, 22, 22, 7, 4, 7, 7, 7, 16, 16, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560791130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560791130 Building ZINC000464434550 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464434550 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/534 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464434550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434550 none COC(=O)C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 50, 50, 50, 37, 37, 4, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/535 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464434550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434550 none COC(=O)C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 50, 50, 50, 39, 39, 4, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464434550 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 Building ZINC000464434550 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464434550 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 534) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464434550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434550 none COC(=O)C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 37, 50, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 13, 13, 13, 13, 50, 50, 50, 37, 37, 4, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 535) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464434550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434550 none COC(=O)C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 14, 14, 50, 50, 50, 39, 39, 4, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464434550 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434550 Building ZINC000464434551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464434551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/536 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464434551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434551 none COC(=O)C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 14, 14, 14, 14, 50, 50, 50, 38, 38, 4, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/537 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464434551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434551 none COC(=O)C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 36, 36, 4, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464434551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 Building ZINC000464434551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464434551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 536) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/536: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464434551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434551 none COC(=O)C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 50, 14, 8, 4, 1, 4, 1, 1, 1, 3, 3, 1, 2, 3, 3, 14, 14, 14, 14, 50, 50, 50, 38, 38, 4, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 537) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/537: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1) `ZINC000464434551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464434551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000464434551 none COC(=O)C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 36, 50, 13, 7, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 13, 50, 50, 50, 36, 36, 4, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464434551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464434551 Building ZINC001287489860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287489860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/538 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287489860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287489860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287489860 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 16, 28, 28, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 28, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/539 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287489860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287489860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287489860 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 16, 27, 27, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 27, 27, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287489860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 Building ZINC001287489860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287489860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 538) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287489860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287489860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287489860 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 16, 28, 28, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 28, 28, 28, 28, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 539) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2) `ZINC001287489860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287489860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287489860 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCOCCNC(=O)[C@]12CCC[C@H]1OCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 8, 16, 27, 27, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 8, 8, 8, 8, 27, 27, 27, 27, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287489860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287489860 Building ZINC001287509070 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287509070 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/540 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/540' -> `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](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287509070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509070 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 15, 37, 37, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/541 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/541' -> `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](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287509070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509070 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 10, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287509070 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 Building ZINC001287509070 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287509070 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 540) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/540: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287509070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509070 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 15, 37, 37, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 37, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 541) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/541: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287509070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509070 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 4, 4, 10, 27, 27, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287509070 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509070 Building ZINC001287509071 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287509071 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/542 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/542' -> `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](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287509071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509071 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 32, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/543 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/543' -> `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](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287509071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509071 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 14, 33, 33, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287509071 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 Building ZINC001287509071 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287509071 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 542) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287509071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509071 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 32, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 543) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1) `ZINC001287509071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287509071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287509071 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](CNC(=O)[C@@H]1OC[C@@H]2CCC[C@@H]21)C1CC1 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', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 14, 33, 33, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11] 50 rigid atoms, others: [33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 40, 41, 36, 38, 37] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287509071 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287509071 Building ZINC001287526219 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287526219 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/544 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287526219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526219 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 43, 49, 35, 43, 30, 35, 12, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 50, 50, 50, 50, 50, 49, 49, 49, 49, 35, 35, 35, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 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, 54, 55, 56]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/545 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287526219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526219 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 35, 44, 27, 35, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 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, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287526219 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 Building ZINC001287526219 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287526219 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 544) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/544: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287526219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526219 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 49, 49, 49, 49, 49, 43, 49, 35, 43, 30, 35, 12, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 37, 37, 50, 50, 50, 50, 50, 49, 49, 49, 49, 35, 35, 35, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37] 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, 54, 55, 56]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 545) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/545: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287526219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526219 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 35, 44, 27, 35, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 36] 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, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287526219 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526219 Building ZINC001287526220 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287526220 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/546 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287526220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526220 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 39, 44, 36, 39, 12, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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, 54, 55, 56]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/547 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287526220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526220 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 38, 45, 33, 38, 13, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 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, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287526220 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 Building ZINC001287526220 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287526220 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 546) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287526220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526220 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 44, 50, 39, 44, 36, 39, 12, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 39, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 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, 54, 55, 56]) total number of confs: 219 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 547) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287526220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287526220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287526220 none CC[C@@H]1CCO[C@@H]1C(=O)N(C)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 45, 50, 38, 45, 33, 38, 13, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33] 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, 54, 55, 56]) total number of confs: 195 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287526220 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287526220 Building ZINC001287531646 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287531646 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/548 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287531646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531646 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 31, 31, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/549 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287531646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531646 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 203 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287531646 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 Building ZINC001287531646 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287531646 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 548) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/548: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287531646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531646 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 30, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 31, 31, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 193 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 549) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/549: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287531646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531646 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 28, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 203 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287531646 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531646 Building ZINC001287531647 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287531647 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/550 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287531647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531647 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/551 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287531647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531647 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 31, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287531647 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 Building ZINC001287531647 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287531647 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 550) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/550: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531647.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287531647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531647 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 30, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 190 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 551) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001287531647.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287531647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001287531647 none CN(C(=O)[C@]12CCC[C@H]1OCC2)[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 31, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56, 57]) total number of confs: 202 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287531647 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287531647 Building ZINC000464578501 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464578501 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/552 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000464578501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464578501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000464578501 none C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 50, 22, 22, 7, 22, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 4, 3, 3, 3, 3, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/553 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000464578501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464578501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000464578501 none C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 50, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464578501 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 Building ZINC000464578501 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000464578501 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 552) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000464578501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000464578501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000464578501 none C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 22, 50, 22, 22, 7, 22, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 4, 3, 3, 3, 3, 22, 22] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 553) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/553: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000464578501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000464578501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000464578501 none C[C@@H]1C[C@H]1N1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 17, 50, 17, 17, 5, 17, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 3, 17, 17, 17, 50, 50, 50, 50, 50, 17, 17, 3, 3, 3, 3, 3, 17, 17] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000464578501 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000464578501 Building ZINC000560978970 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560978970 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/554 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560978970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978970 none CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38] set([35, 36, 17, 18, 19, 20, 21]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/555 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560978970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978970 none CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1] 5 rigid atoms, others: [32, 33, 34, 3, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 38, 29, 30, 31] set([0, 1, 2, 35, 4, 5, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560978970 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 Building ZINC000560978970 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560978970 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 554) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/554: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560978970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978970 none CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38] set([35, 36, 17, 18, 19, 20, 21]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 555) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/555: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560978970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978970 none CN(C)S(=O)(=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1] 5 rigid atoms, others: [32, 33, 34, 3, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 38, 29, 30, 31] set([0, 1, 2, 35, 4, 5, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560978970 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978970 Building ZINC000560978972 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560978972 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/556 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560978972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978972 none CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1] 5 rigid atoms, others: [32, 33, 34, 3, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 38, 29, 30, 31] set([0, 1, 2, 35, 4, 5, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/557 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560978972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978972 none CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38] set([35, 36, 17, 18, 19, 20, 21]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560978972 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 Building ZINC000560978972 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000560978972 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 556) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/556: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000560978972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978972 none CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1] 5 rigid atoms, others: [32, 33, 34, 3, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 38, 29, 30, 31] set([0, 1, 2, 35, 4, 5, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 14 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 557) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/557: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000560978972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000560978972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000560978972 none CN(C)S(=O)(=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1] 2 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38] set([35, 36, 17, 18, 19, 20, 21]) total number of confs: 3 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000560978972 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000560978972 Building ZINC000089682300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/558 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/559 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/560 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/560' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/561 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/561' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 Building ZINC000089682300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 558) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 559) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 560) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 561) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 Building ZINC000089682300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 558) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 559) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 560) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 561) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 Building ZINC000089682300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 558) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 559) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 560) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/560: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 50, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 50, 50, 50, 6, 6] 150 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, 46, 47, 48, 49, 50]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 561) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/561: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682300.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682300 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 28, 28, 28, 28, 28, 28, 28, 28, 32, 49, 49, 48, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 28, 28, 84, 28, 28, 32, 32, 49, 49, 49, 49, 49, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682300 Building ZINC000089682305 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682305 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/562 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/563 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/564 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/564' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/565 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/565' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682305 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 Building ZINC000089682305 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682305 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 562) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 563) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 564) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 565) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682305 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 Building ZINC000089682305 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682305 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 562) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 563) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 564) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 565) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682305 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 Building ZINC000089682305 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682305 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 562) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/562: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 563) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/563: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 564) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/564: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 15, 30, 30, 30, 30, 30, 30, 30, 30, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 30, 30, 90, 30, 30, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 565) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/565: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682305.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682305 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 40, 50, 50, 40, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 34, 34, 102, 34, 34, 40, 40, 50, 50, 40, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682305 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682305 Building ZINC000089682308 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682308 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/566 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/567 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/568 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/568' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/569 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/569' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682308 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 Building ZINC000089682308 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682308 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 566) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 567) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 568) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 569) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682308 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 Building ZINC000089682308 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682308 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 566) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 567) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 568) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 569) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682308 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 Building ZINC000089682308 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682308 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 566) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/566: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 567) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/567: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 568) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/568: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 19, 33, 33, 33, 33, 33, 33, 33, 33, 41, 50, 50, 46, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 10, 10, 33, 33, 99, 33, 33, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 569) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682308.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682308 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 41, 50, 50, 43, 50, 50, 4, 4, 4, 4, 4, 4, 4, 2, 9, 9, 31, 31, 93, 31, 31, 41, 41, 50, 50, 50, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682308 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682308 Building ZINC000089682311 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682311 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/570 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/571 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/572 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/572' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/573 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/573' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682311 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 Building ZINC000089682311 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682311 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 570) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 571) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 572) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 573) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682311 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 Building ZINC000089682311 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682311 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 570) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 571) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 572) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 573) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682311 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 Building ZINC000089682311 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000089682311 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 570) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 571) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/571: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 572) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/572: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 29, 29, 33, 49, 49, 33, 49, 49, 5, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 29, 87, 29, 29, 33, 33, 49, 49, 33, 49, 49, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 573) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/573: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1) `ZINC000089682311.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000089682311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000089682311 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2C[C@@H](O)CN2Cc2ccccc2)cc1 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', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 7, 12, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 26, 33, 50, 50, 33, 50, 50, 6, 6, 6, 6, 6, 6, 6, 3, 12, 12, 26, 26, 78, 26, 26, 33, 33, 50, 50, 33, 50, 50, 6, 6] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089682311 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089682311 Building ZINC000543584779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543584779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/574 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000543584779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543584779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543584779 none O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 10, 15, 15, 15, 20, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 10, 10, 45, 20, 20, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/575 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000543584779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543584779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543584779 none O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 9, 15, 15, 15, 24, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 9, 9, 45, 24, 24, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000543584779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 Building ZINC000543584779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000543584779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 574) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/574: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000543584779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000543584779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543584779 none O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 10, 15, 15, 15, 20, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 10, 10, 45, 20, 20, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 575) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/575: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1) `ZINC000543584779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000543584779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000543584779 none O=C(NC[C@@H](O)COc1ccc(F)c(F)c1)[C@@]([O-])([SiH3])c1ccc(F)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 12, 1, 1, 1, 1, 15, 1, 15, 1, 5, 12, 1, 1, 1, 1, 15, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 3, 3, 9, 15, 15, 15, 24, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 2, 2, 1, 1, 2, 2, 3, 9, 9, 45, 24, 24, 50, 50, 50, 2, 2, 2, 2] 150 rigid atoms, others: [1, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000543584779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000543584779 Building ZINC000489998592 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000489998592 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/576 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 8, 38, 38, 38, 38, 38, 38, 38, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/577 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/578 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/578' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 38, 38, 38, 38, 38, 38, 38, 5, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/579 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/579' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 37, 37, 37, 37, 37, 37, 37, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000489998592 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 Building ZINC000489998592 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000489998592 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 576) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 8, 38, 38, 38, 38, 38, 38, 38, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 577) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 578) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 38, 38, 38, 38, 38, 38, 38, 5, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 579) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 37, 37, 37, 37, 37, 37, 37, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000489998592 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 Building ZINC000489998592 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000489998592 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 576) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 8, 38, 38, 38, 38, 38, 38, 38, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 577) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 578) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 38, 38, 38, 38, 38, 38, 38, 5, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 579) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 37, 37, 37, 37, 37, 37, 37, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000489998592 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 Building ZINC000489998592 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000489998592 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 576) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/576: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 8, 38, 38, 38, 38, 38, 38, 38, 4, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 4, 4, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 577) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/577: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 36, 36, 36, 36, 36, 36, 36, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 578) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/578: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 9, 38, 38, 38, 38, 38, 38, 38, 5, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 5, 5, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 579) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/579: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1) `ZINC000489998592.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000489998592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000489998592 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccn([C@H]3CC[N@@](C)CC3)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 2, 5, 5, 5, 9, 37, 37, 37, 37, 37, 37, 37, 5, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 2, 5, 5, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000489998592 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000489998592 Building ZINC000429278097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429278097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/580 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 32, 32, 32, 10, 10, 10, 10, 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: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/581 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/582 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/582' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 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: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/583 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/583' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000429278097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 Building ZINC000429278097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429278097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 580) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 32, 32, 32, 10, 10, 10, 10, 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: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 581) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 582) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 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: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 583) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000429278097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 Building ZINC000429278097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429278097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 580) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 32, 32, 32, 10, 10, 10, 10, 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: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 581) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 582) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 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: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 583) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000429278097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 Building ZINC000429278097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000429278097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 580) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/580: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 32, 32, 32, 32, 32, 10, 10, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 2, 10, 10, 10, 10, 32, 32, 32, 10, 10, 10, 10, 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: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 581) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/581: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 582) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/582: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 32, 32, 32, 32, 32, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 2, 11, 11, 11, 11, 32, 32, 32, 11, 11, 11, 11, 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: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 583) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/583: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)CC2)cn1) `ZINC000429278097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000429278097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000429278097 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CC[N@@](c3cccnn3)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', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 5, 7, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 10, 10, 5, 5, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 31, 31, 31, 31, 31, 11, 11, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 2, 11, 11, 11, 11, 31, 31, 31, 11, 11, 11, 11, 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: 88 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000429278097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000429278097 Building ZINC000561255770 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561255770 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/584 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/584' -> `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)C1(S(C)(=O)=O)CC1) `ZINC000561255770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561255770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255770 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 12, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 12, 21, 27, 27, 27, 21, 21, 12, 12, 12, 5, 10, 17, 17, 17, 17, 17, 10, 27, 27, 27, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/585 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/585' -> `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)C1(S(C)(=O)=O)CC1) `ZINC000561255770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561255770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255770 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 10, 19, 26, 26, 26, 19, 19, 10, 10, 10, 4, 9, 15, 15, 9, 15, 15, 9, 26, 26, 26, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561255770 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 Building ZINC000561255770 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561255770 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 584) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1) `ZINC000561255770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561255770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255770 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 12, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 12, 21, 27, 27, 27, 21, 21, 12, 12, 12, 5, 10, 17, 17, 17, 17, 17, 10, 27, 27, 27, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 162 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 585) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1) `ZINC000561255770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561255770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255770 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 10, 19, 26, 26, 26, 19, 19, 10, 10, 10, 4, 9, 15, 15, 9, 15, 15, 9, 26, 26, 26, 19, 19, 19, 19] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561255770 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255770 Building ZINC000561255771 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561255771 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/586 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/586' -> `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)C1(S(C)(=O)=O)CC1) `ZINC000561255771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561255771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255771 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 8, 20, 25, 25, 25, 20, 20, 8, 8, 8, 3, 10, 15, 15, 10, 15, 15, 10, 25, 25, 25, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/587 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/587' -> `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)C1(S(C)(=O)=O)CC1) `ZINC000561255771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561255771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255771 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 11, 21, 24, 24, 24, 21, 21, 11, 11, 11, 5, 9, 16, 16, 9, 16, 16, 9, 24, 24, 24, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561255771 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 Building ZINC000561255771 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561255771 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 586) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1) `ZINC000561255771.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561255771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255771 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 8, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 8, 20, 25, 25, 25, 20, 20, 8, 8, 8, 3, 10, 15, 15, 10, 15, 15, 10, 25, 25, 25, 20, 20, 20, 20] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 587) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/587: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1) `ZINC000561255771.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561255771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000561255771 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1)C1(S(C)(=O)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 14, 5, 11, 11, 5, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 16, 16, 9, 11, 21, 24, 24, 24, 21, 21, 11, 11, 11, 5, 9, 16, 16, 9, 16, 16, 9, 24, 24, 24, 21, 21, 21, 21] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 123 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561255771 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561255771 Building ZINC001287586073 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287586073 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/588 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287586073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586073 none C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/589 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287586073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586073 none C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287586073 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 Building ZINC001287586073 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287586073 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 588) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/588: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287586073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586073 none C[C@@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 8, 8, 8, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 589) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/589: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287586073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586073 none C[C@@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 35, 35, 35, 35, 50, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287586073 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586073 Building ZINC001287586074 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287586074 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/590 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287586074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586074 none C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/591 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287586074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586074 none C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287586074 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 Building ZINC001287586074 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287586074 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 590) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/590: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586074.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287586074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586074 none C[C@H](CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 7, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 9, 34, 34, 34, 34, 50, 50, 50, 50, 50, 50, 7, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 591) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1) `ZINC001287586074.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287586074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001287586074 none C[C@H](CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1C[C@H]1C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 10, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287586074 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287586074 Building ZINC000102382955 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382955 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/592 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/593 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/594 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/594' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/595 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/595' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382955 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 Building ZINC000102382955 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382955 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 592) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 593) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 594) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 595) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382955 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 Building ZINC000102382955 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382955 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 592) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 593) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 594) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 595) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382955 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 Building ZINC000102382955 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382955 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 592) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 593) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/593: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 594) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/594: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 595) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/595: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382955.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382955 none COc1cccc(N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 14, 29, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 29, 47, 47, 47, 47, 47, 47, 47, 29, 29, 29, 29, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382955 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382955 Building ZINC000102382958 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382958 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/596 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/597 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/598 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/598' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/599 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/599' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382958 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 Building ZINC000102382958 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382958 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 596) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 597) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 598) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 599) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382958 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 Building ZINC000102382958 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382958 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 596) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 597) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 598) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 599) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382958 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 Building ZINC000102382958 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000102382958 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 596) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 597) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 598) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/598: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 14, 28, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 28, 47, 47, 47, 47, 47, 47, 47, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 47] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 599) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1) `ZINC000102382958.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000102382958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC000102382958 none COc1cccc(N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(C)c3C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 13, 25, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 25, 43, 43, 43, 43, 43, 43, 43, 25, 25, 25, 25, 9, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 43] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000102382958 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000102382958 Building ZINC000277299413 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277299413 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/600 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277299413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299413 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 7, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 31, 31, 31, 31, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/601 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277299413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299413 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 30, 30, 30, 30, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277299413 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 Building ZINC000277299413 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277299413 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 600) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299413.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277299413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299413 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 6, 7, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 31, 31, 31, 31, 14, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 5] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 601) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/601: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299413.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277299413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299413 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 3, 6, 7, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 30, 30, 30, 30, 13, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277299413 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299413 Building ZINC000277299420 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277299420 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/602 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277299420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299420 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 31, 31, 31, 31, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/603 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277299420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299420 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 33, 33, 33, 33, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277299420 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 Building ZINC000277299420 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277299420 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 602) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/602: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277299420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299420 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 31, 31, 31, 31, 12, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 31, 31, 31, 31, 31, 31, 31, 31, 31, 12, 12, 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 603) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/603: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)cn1) `ZINC000277299420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277299420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000277299420 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@]23CCCN(C(=O)OC(C)(C)C)C3)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 33, 33, 33, 33, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277299420 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277299420 Building ZINC000465148396 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465148396 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/604 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465148396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148396 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 31, 31, 31, 26, 26, 11, 11, 11, 4, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/605 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/605' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465148396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148396 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 30, 30, 30, 32, 32, 32, 27, 27, 12, 12, 12, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465148396 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 Building ZINC000465148396 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465148396 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 604) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/604: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465148396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148396 none COC[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 31, 31, 31, 26, 26, 11, 11, 11, 4, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 605) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465148396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148396 none COC[C@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 30, 30, 30, 32, 32, 32, 27, 27, 12, 12, 12, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465148396 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148396 Building ZINC000465148398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465148398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/606 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465148398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148398 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 12, 30, 30, 30, 32, 32, 32, 27, 27, 12, 12, 12, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/607 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465148398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148398 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 31, 31, 31, 26, 26, 11, 11, 11, 4, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465148398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 Building ZINC000465148398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465148398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 606) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465148398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148398 none COC[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 27, 12, 5, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 2, 3, 3, 12, 30, 30, 30, 32, 32, 32, 27, 27, 12, 12, 12, 5, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 607) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC) `ZINC000465148398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465148398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000465148398 none COC[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 11, 4, 11, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 30, 30, 30, 31, 31, 31, 26, 26, 11, 11, 11, 4, 3, 3, 3, 3, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465148398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465148398 Building ZINC000465150930 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465150930 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/608 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465150930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150930 none CCOC(=O)c1sc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 36, 36, 21, 36, 21, 21, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 40, 40, 40, 40, 40, 4, 4, 4, 2, 5, 5, 5, 5, 5, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/609 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/609' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465150930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150930 none CCOC(=O)c1sc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 32, 24, 32, 24, 24, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 37, 37, 37, 37, 37, 4, 4, 4, 2, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465150930 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 Building ZINC000465150930 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465150930 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 608) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465150930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150930 none CCOC(=O)c1sc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 36, 36, 21, 36, 21, 21, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 21, 40, 40, 40, 40, 40, 4, 4, 4, 2, 5, 5, 5, 5, 5, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 609) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/609: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465150930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150930 none CCOC(=O)c1sc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 32, 24, 32, 24, 24, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 37, 37, 37, 37, 37, 4, 4, 4, 2, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465150930 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150930 Building ZINC000465150931 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465150931 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/610 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465150931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150931 none CCOC(=O)c1sc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 32, 24, 32, 24, 24, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 37, 37, 37, 37, 37, 4, 4, 4, 2, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/611 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465150931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150931 none CCOC(=O)c1sc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 35, 35, 21, 35, 21, 21, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 39, 39, 39, 39, 39, 4, 4, 4, 2, 6, 6, 6, 6, 6, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465150931 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 Building ZINC000465150931 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465150931 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 610) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/610: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465150931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150931 none CCOC(=O)c1sc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 32, 32, 24, 32, 24, 24, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 24, 37, 37, 37, 37, 37, 4, 4, 4, 2, 5, 5, 5, 5, 5, 24, 24, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 611) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1sc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C) `ZINC000465150931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465150931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000465150931 none CCOC(=O)c1sc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'S.3', 'C.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', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 14, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 35, 35, 21, 35, 21, 21, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 39, 39, 39, 39, 39, 4, 4, 4, 2, 6, 6, 6, 6, 6, 21, 21, 21] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465150931 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465150931 Building ZINC000927985454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927985454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/612 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)/C(C)=C/CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000927985454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927985454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000927985454 none COC(=O)/C(C)=C/CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 38, 26, 26, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 38, 38, 26, 26, 26, 26, 13, 13, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/613 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)/C(C)=C/CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000927985454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927985454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000927985454 none COC(=O)/C(C)=C/CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 23, 23, 23, 23, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927985454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 Building ZINC000927985454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000927985454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 612) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)/C(C)=C/CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000927985454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000927985454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000927985454 none COC(=O)/C(C)=C/CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 26, 38, 26, 26, 13, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 38, 38, 38, 26, 26, 26, 26, 13, 13, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 142 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 613) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/613: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)/C(C)=C/CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000927985454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000927985454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC000927985454 none COC(=O)/C(C)=C/CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 5, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 36, 23, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 36, 36, 36, 23, 23, 23, 23, 10, 10, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000927985454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000927985454 Building ZINC000465361565 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465361565 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/614 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CNC(=O)C2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000465361565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465361565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000465361565 none O=C(N1CCC2(CNC(=O)C2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 22, 47, 45, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/615 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CNC(=O)C2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000465361565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465361565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000465361565 none O=C(N1CCC2(CNC(=O)C2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 23, 49, 48, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5] 50 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465361565 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 Building ZINC000465361565 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000465361565 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 614) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/614: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CNC(=O)C2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000465361565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000465361565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000465361565 none O=C(N1CCC2(CNC(=O)C2)CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 22, 47, 45, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 5, 5, 1, 5, 5, 5, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 5, 5, 5, 5] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 615) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/615: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CNC(=O)C2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000465361565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000465361565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000465361565 none O=C(N1CCC2(CNC(=O)C2)CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 23, 49, 48, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 5, 5, 1, 1, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5] 50 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]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000465361565 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000465361565 Building ZINC000847274100 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847274100 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/616 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847274100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274100 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 28, 28, 17, 17, 17, 4, 4, 4, 9, 9, 9, 4, 4, 2, 7, 7, 17, 17, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/617 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847274100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274100 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 27, 27, 17, 17, 17, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847274100 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 Building ZINC000847274100 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847274100 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 616) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847274100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274100 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [9, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 28, 28, 17, 17, 17, 4, 4, 4, 9, 9, 9, 4, 4, 2, 7, 7, 17, 17, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 617) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847274100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274100 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [10, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 27, 27, 17, 17, 17, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 17, 17, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847274100 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274100 Building ZINC000847274102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847274102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/618 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847274102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274102 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 18, 18, 18, 18, 28, 28, 18, 18, 18, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 18, 18, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/619 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847274102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274102 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 16, 27, 27, 16, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 16, 16, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847274102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 Building ZINC000847274102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000847274102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 618) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/618: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000847274102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274102 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [10, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 14, 18, 18, 18, 18, 28, 28, 18, 18, 18, 4, 4, 4, 10, 10, 10, 4, 4, 2, 8, 8, 18, 18, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 619) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)cc1Cl) `ZINC000847274102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000847274102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000847274102 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CN(C3CC3)C(=O)O2)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', 'H', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 8, 5, 5, 5, 1, 11, 12, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [8, 4, 2, 4, 4, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 16, 27, 27, 16, 16, 16, 4, 4, 4, 8, 8, 8, 4, 4, 2, 7, 7, 16, 16, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000847274102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000847274102 Building ZINC000277551494 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551494 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/620 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/621 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/622 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/622' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/623 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/623' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551494 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 Building ZINC000277551494 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551494 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 620) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 621) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 622) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 623) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551494 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 Building ZINC000277551494 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551494 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 620) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 621) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 622) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 623) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551494 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 Building ZINC000277551494 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551494 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 620) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 621) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/621: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 7, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 21, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 21, 21, 21, 21, 47, 47, 47, 47, 47, 47, 47, 21, 21] 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: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 622) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 623) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551494.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551494 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 6, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 23, 3, 3, 3, 3, 3, 3, 3, 4, 23, 23, 23, 23, 23, 23, 47, 47, 47, 47, 47, 47, 47, 23, 23] 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: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551494 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551494 Building ZINC000277551495 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551495 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/624 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/625 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/626 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/626' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/627 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/627' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551495 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 Building ZINC000277551495 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551495 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 624) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 625) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 626) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 627) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551495 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 Building ZINC000277551495 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551495 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 624) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 625) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 626) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 627) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551495 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 Building ZINC000277551495 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000277551495 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 624) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 625) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 7, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 19, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 19, 19] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 626) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 627) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/627: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1) `ZINC000277551495.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000277551495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000277551495 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(c2cc(C)nn2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 8, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 22, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277551495 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277551495 Building ZINC000277563125 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563125 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/628 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563125 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 36, 36, 36, 36, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 20, 20, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/629 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563125 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 35, 35, 35, 35, 19, 19, 8, 19, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563125 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 Building ZINC000277563125 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563125 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 628) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563125 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 36, 36, 36, 36, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 36, 36, 36, 36, 36, 36, 36, 36, 36, 20, 20, 20, 20, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 629) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563125 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 28, 35, 35, 35, 35, 19, 19, 8, 19, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 19, 19, 19, 19, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563125 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563125 Building ZINC000277563127 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563127 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/630 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563127 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 29, 29, 34, 34, 34, 34, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/631 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563127 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 29, 29, 34, 34, 34, 34, 21, 21, 7, 21, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563127 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 Building ZINC000277563127 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563127 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 630) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563127 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 29, 29, 34, 34, 34, 34, 21, 21, 6, 21, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 631) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563127 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 29, 29, 34, 34, 34, 34, 21, 21, 7, 21, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 21, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 21, 21, 21, 21, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563127 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563127 Building ZINC000277563129 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563129 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/632 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563129 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 34, 34, 34, 34, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/633 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563129 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 33, 33, 33, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563129 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 Building ZINC000277563129 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563129 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 632) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563129 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 34, 34, 34, 34, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 11, 11, 11, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 633) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563129 none C[C@H]1CN(C(=O)OC(C)(C)C)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 33, 33, 33, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563129 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563129 Building ZINC000277563130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/634 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563130 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 34, 34, 34, 34, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/635 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563130 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 33, 33, 33, 12, 12, 5, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 Building ZINC000277563130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277563130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 634) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277563130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563130 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 34, 34, 34, 34, 12, 12, 7, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 12, 4, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 635) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000277563130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277563130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000277563130 none C[C@@H]1CN(C(=O)OC(C)(C)C)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 33, 33, 33, 33, 12, 12, 5, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 33, 33, 33, 33, 33, 33, 33, 33, 33, 12, 12, 12, 12, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277563130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277563130 Building ZINC000542198866 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542198866 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/636 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn(C)nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542198866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542198866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542198866 none CCOC(=O)c1cn(C)nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 23, 8, 23, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 8, 8, 8, 8, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/637 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn(C)nc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542198866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542198866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542198866 none CCOC(=O)c1cn(C)nc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 24, 9, 24, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000542198866 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 Building ZINC000542198866 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000542198866 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 636) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn(C)nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542198866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000542198866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542198866 none CCOC(=O)c1cn(C)nc1NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 25, 23, 8, 23, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 8, 8, 8, 8, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 637) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cn(C)nc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000542198866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000542198866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000542198866 none CCOC(=O)c1cn(C)nc1NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 5, 8, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 24, 9, 24, 9, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 9, 9, 9, 9, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000542198866 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000542198866 Building ZINC001526302398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526302398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/638 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/639 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/640 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/640' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/641 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/641' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 28, 28, 36, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 28, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526302398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 Building ZINC001526302398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526302398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 638) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 639) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 640) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 641) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 28, 28, 36, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 28, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526302398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 Building ZINC001526302398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526302398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 638) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 639) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 640) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 641) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 28, 28, 36, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 28, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526302398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 Building ZINC001526302398 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001526302398 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 638) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/638: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 639) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/639: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 640) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/640: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 27, 27, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 27, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 641) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/641: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1) `ZINC001526302398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001526302398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001526302398 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CC[C@@H](C(N)=O)C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 15, 28, 28, 36, 49, 49, 49, 49, 49, 49, 50, 50, 49, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 28, 49, 49, 49, 49, 50, 50, 49, 49, 15, 15, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 38, 32, 34, 35, 36, 6, 5, 37, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526302398 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526302398 Building ZINC000277665890 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665890 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/642 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665890 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/643 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665890 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 6, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665890 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 Building ZINC000277665890 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665890 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 642) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/642: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665890 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 643) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665890 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 6, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665890 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665890 Building ZINC000277665894 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665894 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/644 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665894 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/645 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665894 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 10, 10, 10, 10, 10, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665894 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 Building ZINC000277665894 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665894 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 644) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665894.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665894 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 645) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1) `ZINC000277665894.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665894 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 10, 10, 10, 10, 10, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665894 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665894 Building ZINC000277665899 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665899 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/646 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665899 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 6, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/647 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665899 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665899 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 Building ZINC000277665899 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665899 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 646) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665899 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 6, 6, 10, 10, 10, 10, 10, 6, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 647) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/647: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665899 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665899 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665899 Building ZINC000277665903 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665903 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/648 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665903 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 5, 5, 8, 8, 8, 8, 8, 5, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/649 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665903 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665903 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 Building ZINC000277665903 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000277665903 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 648) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000277665903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665903 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 5, 5, 8, 8, 8, 8, 8, 5, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 649) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1) `ZINC000277665903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000277665903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC000277665903 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)C[C@H]2C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 5, 5, 9, 9, 9, 9, 9, 5, 2, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000277665903 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000277665903 Building ZINC000561945267 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561945267 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/650 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1) `ZINC000561945267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561945267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000561945267 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 17, 26, 32, 32, 32, 32, 32, 26, 26, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 13, 13, 26, 26, 26, 26, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/651 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1) `ZINC000561945267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561945267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000561945267 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 19, 27, 34, 34, 34, 34, 34, 27, 27, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 14, 14, 27, 27, 27, 27, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561945267 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 Building ZINC000561945267 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000561945267 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 650) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/650: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1) `ZINC000561945267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000561945267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000561945267 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 17, 26, 32, 32, 32, 32, 32, 26, 26, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 13, 13, 26, 26, 26, 26, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 651) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/651: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1) `ZINC000561945267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000561945267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000561945267 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 2, 2, 2, 14, 27, 27, 19, 27, 34, 34, 34, 34, 34, 27, 27, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 14, 14, 27, 27, 27, 27, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000561945267 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000561945267 Building ZINC000928001931 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928001931 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/652 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928001931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001931 none O=C(N1CC[C@@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 21, 21, 21, 21, 21, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/653 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928001931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001931 none O=C(N1CC[C@@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 21, 21, 21, 21, 21, 48, 48, 48, 48, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 48, 48, 48, 48, 48, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000928001931 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 Building ZINC000928001931 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928001931 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 652) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/652: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928001931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001931 none O=C(N1CC[C@@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 21, 21, 21, 21, 21, 50, 50, 50, 50, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 653) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/653: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928001931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001931 none O=C(N1CC[C@@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 21, 21, 21, 21, 21, 48, 48, 48, 48, 21, 1, 1, 1, 3, 3, 1, 1, 3, 3, 21, 21, 21, 21, 48, 48, 48, 48, 48, 21, 21, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000928001931 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001931 Building ZINC000928001932 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928001932 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/654 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928001932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001932 none O=C(N1CC[C@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 20, 20, 20, 20, 20, 47, 47, 47, 47, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 20, 47, 47, 47, 47, 47, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/655 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928001932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001932 none O=C(N1CC[C@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 24, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000928001932 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 Building ZINC000928001932 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928001932 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 654) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/654: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928001932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001932 none O=C(N1CC[C@H](C2OCCO2)C1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 8, 20, 20, 20, 20, 20, 47, 47, 47, 47, 20, 1, 1, 1, 3, 3, 1, 1, 3, 3, 20, 20, 20, 20, 47, 47, 47, 47, 47, 20, 20, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 655) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/655: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000928001932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928001932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000928001932 none O=C(N1CC[C@H](C2OCCO2)C1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 7, 24, 24, 24, 24, 24, 50, 50, 50, 50, 24, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 24, 24, 50, 50, 50, 50, 50, 24, 24, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000928001932 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000928001932 Building ZINC001526329658 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526329658 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/656 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/656' -> `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(Cc1cccc(C(N)=O)c1)C1CC1) `ZINC001526329658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526329658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526329658 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 11, 1, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 14, 30, 30, 30, 30, 30, 37, 37, 30, 6, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 30, 30, 30, 37, 37, 30, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/657 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/657' -> `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(Cc1cccc(C(N)=O)c1)C1CC1) `ZINC001526329658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526329658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526329658 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 11, 1, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 16, 30, 30, 30, 30, 30, 37, 37, 29, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 30, 37, 37, 30, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526329658 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 Building ZINC001526329658 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526329658 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 656) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/656: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1) `ZINC001526329658.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526329658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526329658 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 11, 1, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 14, 30, 30, 30, 30, 30, 37, 37, 30, 6, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 30, 30, 30, 37, 37, 30, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 125 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 657) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1) `ZINC001526329658.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526329658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001526329658 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(C(N)=O)c1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 11, 1, 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] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 7, 16, 30, 30, 30, 30, 30, 37, 37, 29, 7, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 30, 30, 30, 37, 37, 30, 11, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526329658 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526329658 Building ZINC001526383064 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526383064 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/658 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001526383064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526383064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001526383064 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 11, 11, 7, 7, 7, 15, 15, 15, 15, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 11, 11, 7, 15, 15, 15, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/659 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001526383064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526383064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001526383064 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 11, 11, 7, 7, 7, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 11, 11, 7, 14, 14, 14, 6] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526383064 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 Building ZINC001526383064 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526383064 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 658) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001526383064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526383064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001526383064 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 7, 4, 7, 11, 11, 7, 7, 7, 15, 15, 15, 15, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 11, 11, 7, 15, 15, 15, 6] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 659) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1) `ZINC001526383064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526383064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 45 natoms 44 natoms 43 natoms 42 names: ZINC001526383064 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2n2ccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 11, 11, 7, 7, 7, 14, 14, 14, 14, 6, 6, 11, 11, 11, 11, 11, 6, 2, 7, 7, 11, 11, 7, 14, 14, 14, 6] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526383064 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526383064 Building ZINC000089990011 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000089990011 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/660 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1) `ZINC000089990011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089990011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000089990011 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 8, 24, 24, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/661 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1) `ZINC000089990011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089990011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000089990011 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 8, 24, 24, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089990011 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 Building ZINC000089990011 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000089990011 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 660) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1) `ZINC000089990011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000089990011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000089990011 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 8, 24, 24, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 661) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/661: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1) `ZINC000089990011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000089990011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000089990011 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c[nH]cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 6, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 11, 11, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 11, 8, 24, 24, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000089990011 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000089990011 Building ZINC000090122584 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000090122584 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/662 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1) `ZINC000090122584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000090122584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000090122584 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 8, 1, 17, 1, 8, 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, 3, 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: [34, 11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 34, 34, 34, 34, 34, 11, 4, 12, 12, 12, 12, 12, 11] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/663 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1) `ZINC000090122584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000090122584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000090122584 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 8, 1, 17, 1, 8, 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, 3, 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: [34, 11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 34, 34, 34, 34, 34, 11, 4, 12, 12, 12, 12, 12, 11] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000090122584 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 Building ZINC000090122584 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000090122584 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 662) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/662: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1) `ZINC000090122584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000090122584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000090122584 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 8, 1, 17, 1, 8, 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, 3, 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: [34, 11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 34, 34, 34, 34, 34, 11, 4, 12, 12, 12, 12, 12, 11] 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 663) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/663: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1) `ZINC000090122584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000090122584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 37 natoms 36 natoms 35 natoms 34 names: ZINC000090122584 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)nc2Br)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'N.ar', 'C.ar', 'Br', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 8, 1, 17, 1, 8, 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, 3, 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: [34, 11, 11, 11, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 34, 34, 34, 34, 34, 11, 4, 12, 12, 12, 12, 12, 11] 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]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000090122584 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000090122584 Building ZINC000091085722 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000091085722 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/664 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/664' -> `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)NCc1ccnc(OCC(F)F)c1) `ZINC000091085722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000091085722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000091085722 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 23, 23, 23, 39, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 50, 50, 50, 23] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/665 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/665' -> `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)NCc1ccnc(OCC(F)F)c1) `ZINC000091085722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000091085722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000091085722 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 24, 24, 24, 24, 24, 40, 50, 50, 50, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 24, 24, 50, 50, 50, 24] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000091085722 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 Building ZINC000091085722 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000091085722 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 664) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/664: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1) `ZINC000091085722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000091085722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000091085722 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 23, 23, 23, 39, 50, 50, 50, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 50, 50, 50, 23] 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]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 665) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/665: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1) `ZINC000091085722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000091085722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000091085722 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccnc(OCC(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 10, 24, 24, 24, 24, 24, 40, 50, 50, 50, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 24, 24, 50, 50, 50, 24] 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000091085722 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000091085722 Building ZINC001526393857 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526393857 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/666 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ncc1I) `ZINC001526393857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526393857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526393857 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ncc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 21] 45 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/667 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ncc1I) `ZINC001526393857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526393857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526393857 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ncc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 21] 45 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526393857 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 Building ZINC001526393857 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526393857 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 666) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ncc1I) `ZINC001526393857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526393857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526393857 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ncc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 21] 45 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 667) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ncc1I) `ZINC001526393857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526393857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001526393857 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ncc1I NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.ar', 'I', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 18, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 12, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 21] 45 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526393857 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526393857 Building ZINC000092526690 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092526690 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/668 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1) `ZINC000092526690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092526690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000092526690 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 13, 13, 6, 7, 40, 40, 40, 41, 40, 40, 13, 13, 9, 9, 9, 9, 9, 9, 9, 5, 13, 13, 41, 40, 42, 41, 13, 13, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/669 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1) `ZINC000092526690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092526690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000092526690 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 14, 14, 5, 5, 39, 39, 39, 39, 39, 39, 14, 14, 9, 9, 9, 9, 9, 9, 9, 5, 14, 14, 39, 39, 39, 39, 14, 14, 9, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000092526690 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 Building ZINC000092526690 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000092526690 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 668) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1) `ZINC000092526690.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000092526690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000092526690 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 13, 13, 6, 7, 40, 40, 40, 41, 40, 40, 13, 13, 9, 9, 9, 9, 9, 9, 9, 5, 13, 13, 41, 40, 42, 41, 13, 13, 9, 9] 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]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 669) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1) `ZINC000092526690.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000092526690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000092526690 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(n3ncn(C)c3=O)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 5, 1, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 1, 5, 5, 5, 14, 14, 5, 5, 39, 39, 39, 39, 39, 39, 14, 14, 9, 9, 9, 9, 9, 9, 9, 5, 14, 14, 39, 39, 39, 39, 14, 14, 9, 9] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000092526690 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000092526690 Building ZINC000652540582 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652540582 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/670 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1) `ZINC000652540582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652540582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000652540582 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1 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', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 26, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 26, 26, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/671 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1) `ZINC000652540582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652540582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000652540582 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1 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', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 3, 4, 4, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 17, 17, 41, 41, 41, 41, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000652540582 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 Building ZINC000652540582 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652540582 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 670) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/670: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1) `ZINC000652540582.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652540582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000652540582 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1 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', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 26, 49, 49, 49, 49, 49, 49, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 26, 26, 49, 49, 49, 49, 5, 5] 50 rigid atoms, others: [5, 6, 7] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 671) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1) `ZINC000652540582.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652540582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000652540582 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1CCn2c(Cc3cccc(F)c3)nnc2C1 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', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 1, 1, 1, 1, 1, 15, 1, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 3, 3, 4, 4, 4, 4, 4, 17, 41, 41, 41, 41, 41, 41, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 17, 17, 41, 41, 41, 41, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000652540582 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000652540582 Building ZINC001082753884 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001082753884 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/672 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001082753884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001082753884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001082753884 none COC(=O)CN(Cc1ccccc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 4, 2, 4, 17, 23, 23, 22, 23, 22, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 11, 11, 17, 17, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/673 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001082753884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001082753884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001082753884 none COC(=O)CN(Cc1ccccc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 5, 2, 5, 18, 24, 24, 23, 24, 23, 24, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 12, 12, 18, 18, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001082753884 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 Building ZINC001082753884 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001082753884 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 672) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001082753884.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001082753884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001082753884 none COC(=O)CN(Cc1ccccc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 11, 22, 4, 2, 4, 17, 23, 23, 22, 23, 22, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 11, 11, 17, 17, 23, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 153 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 673) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/673: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CN(Cc1ccccc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC001082753884.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001082753884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001082753884 none COC(=O)CN(Cc1ccccc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 5, 2, 5, 18, 24, 24, 23, 24, 23, 24, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 12, 12, 18, 18, 24, 24, 24, 24, 24, 24, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001082753884 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001082753884 Building ZINC000171863833 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171863833 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/674 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/675 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/676 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/676' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/677 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/677' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171863833 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 Building ZINC000171863833 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171863833 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 674) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 675) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 676) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 677) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171863833 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 Building ZINC000171863833 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171863833 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 674) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 675) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 676) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 677) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171863833 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 Building ZINC000171863833 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171863833 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 674) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/674: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 675) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/675: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 29, 13, 13, 13, 13, 13, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 29, 29, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 676) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/676: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 677) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1) `ZINC000171863833.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171863833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000171863833 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 12, 12, 12, 12, 12, 6, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 27, 27, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171863833 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171863833 Building ZINC000171864083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171864083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/678 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/679 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/680 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/680' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/681 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/681' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171864083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 Building ZINC000171864083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171864083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 678) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 679) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 680) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 681) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171864083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 Building ZINC000171864083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171864083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 678) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 679) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 680) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 681) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171864083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 Building ZINC000171864083 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000171864083 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 678) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 679) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/679: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 17, 11, 11, 11, 11, 11, 7, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 11, 11, 28, 28, 28, 28, 28, 17, 17, 11, 11, 11, 11, 11, 11, 2, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 680) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/680: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 681) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/681: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1) `ZINC000171864083.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000171864083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000171864083 none Cc1nc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)CC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 17, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 10, 10, 30, 30, 30, 30, 30, 17, 17, 10, 10, 10, 10, 10, 10, 2, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000171864083 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000171864083 Building ZINC000172116598 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172116598 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/682 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2cncn2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172116598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116598 none O=C(N1CCC[C@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 1, 1, 1, 9, 9, 9, 9, 10, 10, 9, 10, 10, 9, 10, 10, 10, 10, 10, 10, 32, 32, 10, 10, 9, 10, 10, 9, 10, 10, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/683 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2cncn2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172116598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116598 none O=C(N1CCC[C@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 9, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 14, 14, 14, 14, 14, 14, 32, 32, 14, 14, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172116598 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 Building ZINC000172116598 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172116598 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 682) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2cncn2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172116598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116598 none O=C(N1CCC[C@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 10, 10, 10, 10, 10, 10, 32, 32, 32, 32, 10, 1, 1, 1, 9, 9, 9, 9, 10, 10, 9, 10, 10, 9, 10, 10, 10, 10, 10, 10, 32, 32, 10, 10, 9, 10, 10, 9, 10, 10, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 683) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H](n2cncn2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172116598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116598 none O=C(N1CCC[C@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 9, 14, 14, 14, 14, 14, 14, 32, 32, 32, 32, 14, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 14, 14, 14, 14, 14, 14, 32, 32, 14, 14, 6, 8, 8, 6, 8, 8, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172116598 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116598 Building ZINC000172116602 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172116602 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/684 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2cncn2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172116602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116602 none O=C(N1CCC[C@@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 7, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 30, 30, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/685 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2cncn2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172116602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116602 none O=C(N1CCC[C@@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 8, 11, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 11, 11, 11, 11, 11, 11, 31, 31, 11, 11, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172116602 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 Building ZINC000172116602 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172116602 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 684) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/684: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2cncn2)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172116602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116602 none O=C(N1CCC[C@@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 7, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 11, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 11, 11, 11, 11, 11, 11, 30, 30, 11, 11, 6, 9, 9, 9, 9, 9, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 685) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/685: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H](n2cncn2)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000172116602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172116602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000172116602 none O=C(N1CCC[C@@H](n2cncn2)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.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 5, 5, 5, 5, 7, 8, 1, 8, 1, 8, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 8, 11, 11, 11, 11, 11, 11, 31, 31, 31, 31, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 11, 11, 11, 11, 11, 11, 31, 31, 11, 11, 6, 11, 11, 6, 11, 11, 6] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172116602 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172116602 Building ZINC000172704454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172704454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/686 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172704454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704454 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25, 36, 36, 36, 25, 25, 25, 8, 8, 8, 4, 6, 6, 6, 6, 6, 25, 25, 36, 36, 36, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/687 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172704454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704454 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 29, 29, 29, 29, 36, 36, 36, 29, 29, 29, 8, 8, 8, 4, 6, 6, 6, 6, 6, 29, 29, 36, 36, 36, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172704454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 Building ZINC000172704454 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172704454 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 686) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704454.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172704454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704454 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25, 36, 36, 36, 25, 25, 25, 8, 8, 8, 4, 6, 6, 6, 6, 6, 25, 25, 36, 36, 36, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 687) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704454.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172704454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704454 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 29, 29, 29, 29, 36, 36, 36, 29, 29, 29, 8, 8, 8, 4, 6, 6, 6, 6, 6, 29, 29, 36, 36, 36, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172704454 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704454 Building ZINC000172704457 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172704457 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/688 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172704457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704457 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 29, 29, 29, 29, 36, 36, 36, 29, 29, 29, 8, 8, 8, 4, 6, 6, 6, 6, 6, 29, 29, 36, 36, 36, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/689 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172704457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704457 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25, 36, 36, 36, 25, 25, 25, 8, 8, 8, 4, 6, 6, 6, 6, 6, 25, 25, 36, 36, 36, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172704457 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 Building ZINC000172704457 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172704457 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 688) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172704457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704457 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 29, 29, 29, 29, 36, 36, 36, 29, 29, 29, 8, 8, 8, 4, 6, 6, 6, 6, 6, 29, 29, 36, 36, 36, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 689) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1) `ZINC000172704457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172704457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000172704457 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1ccc(S(C)(=O)=O)c(F)c1 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.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 14, 5, 11, 11, 1, 15, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 25, 25, 25, 25, 36, 36, 36, 25, 25, 25, 8, 8, 8, 4, 6, 6, 6, 6, 6, 25, 25, 36, 36, 36, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172704457 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172704457 Building ZINC000172749698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000172749698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/690 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/691 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/692 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/692' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/693 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/693' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172749698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 Building ZINC000172749698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000172749698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 690) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 691) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 692) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 693) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172749698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 Building ZINC000172749698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000172749698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 690) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 691) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 692) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 693) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172749698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 Building ZINC000172749698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000172749698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 690) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/690: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 691) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/691: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 22, 48, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 692) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/692: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1) `ZINC000172749698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 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, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 161 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 693) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/693: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1) `ZINC000172749698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000172749698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000172749698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@]2(N3CCCCC3)CC[N@](C)CC2)cc1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 6, 6, 1, 1, 1, 1, 3, 3, 3, 21, 47, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000172749698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000172749698 Building ZINC000177612918 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177612918 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/694 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21) `ZINC000177612918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177612918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612918 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 7, 7, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 7, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/695 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21) `ZINC000177612918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177612918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612918 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 4, 7, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177612918 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 Building ZINC000177612918 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177612918 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 694) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/694: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21) `ZINC000177612918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177612918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612918 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 7, 7, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 7, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 101 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 695) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/695: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21) `ZINC000177612918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177612918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612918 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 7, 7, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 4, 7, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177612918 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612918 Building ZINC000177612934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177612934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/696 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21) `ZINC000177612934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177612934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612934 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 8, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/697 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21) `ZINC000177612934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177612934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612934 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177612934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 Building ZINC000177612934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177612934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 696) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/696: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21) `ZINC000177612934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177612934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612934 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 6, 13, 13, 4, 4, 1, 1, 1, 1, 8, 8, 8, 29, 29, 29, 29, 29, 29, 29, 29, 29, 4, 4, 4, 13, 13, 8, 13, 13, 4, 4, 4, 8, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 107 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 697) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/697: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21) `ZINC000177612934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177612934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000177612934 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCn2ncnc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 7, 7, 7, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4, 4, 4, 12, 12, 4, 12, 12, 4, 4, 4, 7, 28, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177612934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177612934 Building ZINC000177703203 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177703203 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/698 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177703203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703203 none Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/699 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/699' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177703203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703203 none Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 11, 19, 19, 11, 19, 19, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177703203 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 Building ZINC000177703203 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177703203 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 698) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177703203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703203 none Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 699) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177703203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703203 none Cc1nc2n(n1)CCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 16, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 19, 19, 11, 19, 19, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 11, 19, 19, 11, 19, 19, 11] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177703203 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703203 Building ZINC000177703217 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177703217 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/700 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177703217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703217 none Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 16, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/701 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177703217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703217 none Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177703217 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 Building ZINC000177703217 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177703217 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 700) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/700: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177703217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703217 none Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 16, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 19, 19, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 12, 19, 19, 12, 19, 19, 12] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 701) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/701: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000177703217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177703217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000177703217 none Cc1nc2n(n1)CCC[C@H]2NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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: [5, 1, 8, 1, 8, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 14, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000177703217 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000177703217 Building ZINC001350702086 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350702086 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/702 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350702086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350702086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001350702086 none CCOCCOC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 19, 10, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 4, 4, 34, 34, 34, 34, 34, 23, 23, 19, 19, 4, 4, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/703 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/703' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350702086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350702086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001350702086 none CCOCCOC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 36, 36, 36, 36, 36, 25, 25, 23, 23, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350702086 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 Building ZINC001350702086 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350702086 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 702) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350702086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350702086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001350702086 none CCOCCOC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 19, 10, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 8, 8, 8, 5, 4, 4, 34, 34, 34, 34, 34, 23, 23, 19, 19, 4, 4, 4, 4, 4, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 703) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1) `ZINC001350702086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350702086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001350702086 none CCOCCOC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 8, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 2, 4, 4, 36, 36, 36, 36, 36, 25, 25, 23, 23, 4, 4, 4, 4, 4, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350702086 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350702086 Building ZINC000178722906 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178722906 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/704 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C) `ZINC000178722906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178722906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000178722906 none CNC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 20, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 6, 19, 17, 20, 20, 20, 20, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/705 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C) `ZINC000178722906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178722906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000178722906 none CNC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 7, 18, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 7, 21, 20, 18, 18, 18, 18, 2, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000178722906 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 Building ZINC000178722906 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178722906 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 704) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/704: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C) `ZINC000178722906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178722906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000178722906 none CNC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 20, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 4, 4, 6, 19, 17, 20, 20, 20, 20, 2, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 137 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 705) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/705: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C) `ZINC000178722906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178722906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000178722906 none CNC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 7, 18, 2, 7, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 7, 21, 20, 18, 18, 18, 18, 2, 4, 4, 4, 9, 9, 8, 9, 9, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000178722906 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000178722906 Building ZINC001287788696 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287788696 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/706 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287788696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287788696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788696 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 16, 39, 16, 16, 9, 4, 1, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 16, 9, 9, 9, 9, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 44, 45, 46, 47, 16, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/707 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/707' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287788696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287788696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788696 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 23, 42, 23, 23, 12, 6, 2, 6, 6, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 23, 12, 12, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287788696 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 Building ZINC001287788696 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287788696 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 706) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287788696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287788696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788696 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 16, 39, 16, 16, 9, 4, 1, 4, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 16, 9, 9, 9, 9, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 44, 45, 46, 47, 16, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 198 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 707) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287788696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287788696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788696 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 23, 42, 23, 23, 12, 6, 2, 6, 6, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 42, 42, 23, 12, 12, 11, 11, 33, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287788696 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788696 Building ZINC001287788697 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287788697 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/708 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287788697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287788697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788697 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 18, 39, 18, 18, 11, 6, 2, 6, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 18, 11, 11, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/709 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287788697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287788697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788697 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 18, 40, 18, 18, 8, 4, 1, 4, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 40, 18, 8, 8, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 44, 45, 46, 47, 16, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287788697 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 Building ZINC001287788697 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287788697 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 708) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/708: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001287788697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287788697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788697 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 18, 39, 18, 18, 11, 6, 2, 6, 6, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 39, 39, 18, 11, 11, 10, 10, 30, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [45, 46, 47, 48, 49, 50, 51, 52, 21, 23, 24, 25, 26, 27, 28, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 709) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001287788697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287788697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001287788697 none Cc1ccccc1[C@@H]1C[C@H]1C(=O)NC[C@H](CO)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 40, 40, 40, 40, 18, 40, 18, 18, 8, 4, 1, 4, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 40, 18, 8, 8, 10, 10, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [48, 44, 45, 46, 47, 16, 49, 50, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287788697 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287788697 Building ZINC000179166478 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179166478 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/710 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1) `ZINC000179166478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179166478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000179166478 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 16, 17, 22, 22, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 8, 16, 16, 17, 17, 22, 22, 22, 22, 22, 22, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/711 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/711' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1) `ZINC000179166478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179166478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000179166478 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 15, 15, 21, 21, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 8, 15, 15, 15, 15, 21, 21, 21, 21, 21, 21, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179166478 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 Building ZINC000179166478 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179166478 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 710) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1) `ZINC000179166478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179166478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000179166478 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 16, 17, 22, 22, 4, 5, 5, 10, 10, 10, 10, 10, 5, 2, 4, 4, 4, 8, 16, 16, 17, 17, 22, 22, 22, 22, 22, 22, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 711) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1) `ZINC000179166478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179166478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000179166478 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2cccc(C(=O)NCCN(C)C)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 8, 8, 8, 15, 15, 21, 21, 4, 5, 5, 11, 11, 11, 11, 11, 5, 2, 4, 4, 4, 8, 15, 15, 15, 15, 21, 21, 21, 21, 21, 21, 4, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179166478 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179166478 Building ZINC000179257774 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179257774 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/712 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1) `ZINC000179257774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179257774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000179257774 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 17, 17, 17, 17, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/713 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1) `ZINC000179257774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179257774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000179257774 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 17, 17, 17, 17, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179257774 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 Building ZINC000179257774 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179257774 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 712) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/712: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1) `ZINC000179257774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179257774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000179257774 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 23, 23, 23, 23, 23, 23, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 17, 17, 17, 17, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 713) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1) `ZINC000179257774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179257774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000179257774 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccc2Oc2cnccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 9, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 17, 17, 17, 17, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179257774 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179257774 Building ZINC000179277523 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277523 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/714 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277523 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 13, 13, 8, 11, 20, 20, 20, 20, 20, 20, 20, 13, 13, 6, 6, 11, 11, 11, 11, 11, 6, 4, 6, 6, 6, 13, 13, 20, 20, 20, 20, 20, 20, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/715 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277523 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 11, 11, 5, 7, 17, 17, 17, 17, 17, 17, 17, 11, 11, 6, 6, 10, 10, 10, 10, 10, 6, 3, 5, 5, 5, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277523 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 Building ZINC000179277523 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277523 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 714) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277523 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 13, 13, 8, 11, 20, 20, 20, 20, 20, 20, 20, 13, 13, 6, 6, 11, 11, 11, 11, 11, 6, 4, 6, 6, 6, 13, 13, 20, 20, 20, 20, 20, 20, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 715) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/715: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277523 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 11, 11, 5, 7, 17, 17, 17, 17, 17, 17, 17, 11, 11, 6, 6, 10, 10, 10, 10, 10, 6, 3, 5, 5, 5, 11, 11, 17, 17, 17, 17, 17, 17, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 92 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277523 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277523 Building ZINC000179277530 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277530 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/716 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277530 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 13, 13, 7, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 4, 7, 7, 7, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/717 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277530 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 9, 10, 18, 18, 18, 18, 18, 18, 18, 15, 15, 6, 6, 14, 14, 14, 14, 14, 6, 4, 8, 8, 8, 15, 15, 18, 18, 18, 18, 18, 18, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277530 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 Building ZINC000179277530 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277530 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 716) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/716: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277530 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 13, 13, 7, 13, 17, 17, 17, 17, 17, 17, 17, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 4, 7, 7, 7, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 717) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/717: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1) `ZINC000179277530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277530 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 9, 10, 18, 18, 18, 18, 18, 18, 18, 15, 15, 6, 6, 14, 14, 14, 14, 14, 6, 4, 8, 8, 8, 15, 15, 18, 18, 18, 18, 18, 18, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277530 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277530 Building ZINC000179277538 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277538 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/718 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277538 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 15, 15, 7, 7, 13, 13, 13, 13, 13, 7, 4, 8, 8, 8, 15, 15, 18, 18, 18, 18, 18, 18, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/719 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/719' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277538 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 13, 13, 7, 7, 17, 17, 17, 17, 17, 17, 17, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 4, 7, 7, 7, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277538 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 Building ZINC000179277538 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277538 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 718) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277538 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 15, 15, 8, 8, 18, 18, 18, 18, 18, 18, 18, 15, 15, 7, 7, 13, 13, 13, 13, 13, 7, 4, 8, 8, 8, 15, 15, 18, 18, 18, 18, 18, 18, 15, 15, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 719) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277538 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 13, 13, 7, 7, 17, 17, 17, 17, 17, 17, 17, 13, 13, 6, 6, 14, 14, 14, 14, 14, 6, 4, 7, 7, 7, 13, 13, 17, 17, 17, 17, 17, 17, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277538 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277538 Building ZINC000179277547 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277547 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/720 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277547 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 12, 12, 8, 8, 18, 18, 18, 18, 18, 18, 18, 12, 12, 6, 6, 10, 10, 10, 10, 10, 6, 4, 6, 6, 6, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/721 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277547 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 13, 13, 7, 8, 19, 19, 19, 19, 19, 19, 19, 13, 13, 7, 7, 12, 12, 12, 12, 12, 7, 4, 6, 6, 6, 13, 13, 19, 19, 19, 19, 19, 19, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277547 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 Building ZINC000179277547 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179277547 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 720) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/720: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179277547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277547 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 12, 12, 8, 8, 18, 18, 18, 18, 18, 18, 18, 12, 12, 6, 6, 10, 10, 10, 10, 10, 6, 4, 6, 6, 6, 12, 12, 18, 18, 18, 18, 18, 18, 12, 12, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 721) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/721: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1) `ZINC000179277547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179277547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 53 natoms 52 natoms 51 natoms 50 names: ZINC000179277547 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)c2ccc(N3C(=O)NC[C@@H]3C)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 13, 13, 7, 8, 19, 19, 19, 19, 19, 19, 19, 13, 13, 7, 7, 12, 12, 12, 12, 12, 7, 4, 6, 6, 6, 13, 13, 19, 19, 19, 19, 19, 19, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179277547 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179277547 Building ZINC000179487905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179487905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/722 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/723 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/724 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/724' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/725 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/725' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179487905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 Building ZINC000179487905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179487905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 722) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 723) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 724) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 725) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179487905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 Building ZINC000179487905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179487905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 722) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 723) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 724) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 725) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179487905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 Building ZINC000179487905 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000179487905 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 722) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 723) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 724) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/724: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 14, 14, 14, 14, 30, 30, 14, 5, 5, 2, 2, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 5, 10, 10, 30, 30, 30, 30, 30, 5, 5, 5, 5, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 725) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/725: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1) `ZINC000179487905.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000179487905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000179487905 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCN(Cc3noc(C4CC4)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 8, 12, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 4, 4, 6, 6, 6, 6, 6, 11, 15, 15, 15, 15, 26, 26, 15, 6, 6, 2, 2, 6, 6, 6, 6, 6, 2, 6, 6, 6, 6, 6, 6, 11, 11, 26, 26, 26, 26, 26, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179487905 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179487905 Building ZINC000179517297 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179517297 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/726 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1) `ZINC000179517297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179517297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC000179517297 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/727 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1) `ZINC000179517297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179517297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC000179517297 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 4, 4, 4, 4, 4, 2, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179517297 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 Building ZINC000179517297 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179517297 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 726) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1) `ZINC000179517297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179517297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC000179517297 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 2, 4, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 727) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1) `ZINC000179517297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179517297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 48 natoms 47 natoms 46 natoms 45 names: ZINC000179517297 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc4ccccc4o3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 3, 7, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 2, 2, 4, 4, 4, 4, 4, 2, 8, 8, 8, 8, 15, 15, 15, 15, 8, 8, 8, 8, 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179517297 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179517297 Building ZINC000792521596 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000792521596 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/728 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000792521596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521596 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 21, 27, 29, 29, 34, 34, 34, 34, 21, 21, 21, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/729 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000792521596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521596 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 24, 31, 34, 34, 37, 37, 37, 37, 24, 24, 24, 13, 13, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000792521596 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 Building ZINC000792521596 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000792521596 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 728) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521596.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000792521596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521596 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 10, 10, 10, 6, 21, 27, 29, 29, 34, 34, 34, 34, 21, 21, 21, 12, 12, 2, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 27, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 729) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521596.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000792521596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521596 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 24, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 24, 31, 34, 34, 37, 37, 37, 37, 24, 24, 24, 13, 13, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000792521596 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521596 Building ZINC000792521597 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000792521597 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/730 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000792521597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521597 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 24, 28, 31, 31, 38, 38, 38, 38, 24, 24, 24, 14, 14, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/731 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000792521597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521597 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 21, 26, 28, 28, 34, 34, 34, 34, 21, 21, 21, 13, 13, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000792521597 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 Building ZINC000792521597 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000792521597 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 730) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/730: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000792521597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521597 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 6, 24, 28, 31, 31, 38, 38, 38, 38, 24, 24, 24, 14, 14, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 28, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 731) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/731: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C) `ZINC000792521597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000792521597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000792521597 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 21, 26, 28, 28, 34, 34, 34, 34, 21, 21, 21, 13, 13, 2, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 26, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000792521597 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000792521597 Building ZINC001287804730 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287804730 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/732 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)OCCCO2) `ZINC001287804730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287804730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001287804730 none COC(=O)c1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 8, 14, 14, 14, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 4, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/733 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)OCCCO2) `ZINC001287804730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287804730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001287804730 none COC(=O)c1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 8, 14, 14, 14, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 4, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287804730 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 Building ZINC001287804730 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001287804730 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 732) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/732: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)OCCCO2) `ZINC001287804730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001287804730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001287804730 none COC(=O)c1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 8, 14, 14, 14, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 4, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 733) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/733: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)OCCCO2) `ZINC001287804730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001287804730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001287804730 none COC(=O)c1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)OCCCO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 5, 5, 5, 12, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 31, 8, 14, 14, 14, 8, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 31, 31, 31, 14, 14, 4, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001287804730 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001287804730 Building ZINC000179955173 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955173 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/734 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955173 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 11, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 30, 30, 11, 30, 4] 150 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]) total number of confs: 123 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/735 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955173 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 9, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 9, 9, 27, 9, 9, 30, 30, 9, 30, 6] 150 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]) total number of confs: 117 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955173 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 Building ZINC000179955173 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955173 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 734) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/734: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955173 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 11, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 30, 30, 11, 30, 4] 150 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]) total number of confs: 123 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 735) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/735: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955173 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 9, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 9, 9, 27, 9, 9, 30, 30, 9, 30, 6] 150 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]) total number of confs: 117 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955173 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955173 Building ZINC000179955187 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955187 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/736 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955187 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 28, 28, 18, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 28, 28, 18, 28, 4] 150 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/737 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955187 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 30, 30, 8, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 8, 8, 24, 8, 8, 30, 30, 8, 30, 6] 150 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955187 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 Building ZINC000179955187 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955187 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 736) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955187 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 28, 28, 18, 28, 28, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 28, 28, 18, 28, 4] 150 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 737) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955187 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 30, 30, 8, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 8, 8, 24, 8, 8, 30, 30, 8, 30, 6] 150 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955187 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955187 Building ZINC000179955202 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955202 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/738 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955202 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 30, 30, 13, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 8, 8, 24, 8, 8, 30, 30, 30, 30, 6] 150 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/739 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955202 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 11, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 29, 29, 11, 29, 4] 150 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955202 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 Building ZINC000179955202 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955202 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 738) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955202 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 30, 30, 13, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 6, 6, 8, 8, 24, 8, 8, 30, 30, 30, 30, 6] 150 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 739) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955202 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 11, 29, 29, 29, 29, 29, 29, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 29, 29, 11, 29, 4] 150 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955202 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955202 Building ZINC000179955223 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955223 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/740 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955223 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 9, 9, 27, 9, 9, 29, 29, 29, 29, 6] 150 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]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/741 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955223 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 11, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 30, 30, 11, 30, 4] 150 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]) total number of confs: 123 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955223 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 Building ZINC000179955223 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179955223 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 740) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/740: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179955223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955223 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 6, 6, 9, 9, 27, 9, 9, 29, 29, 29, 29, 6] 150 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]) total number of confs: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 741) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/741: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)cn1) `ZINC000179955223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179955223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000179955223 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H](O)C[C@H]2c2cccc(C(F)(F)F)c2)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', 'O.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'N.2', '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, 12, 5, 5, 7, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 11, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 4, 11, 11, 33, 11, 11, 30, 30, 11, 30, 4] 150 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]) total number of confs: 123 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000179955223 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000179955223 Building ZINC000180721678 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721678 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/742 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/743 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/744 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/744' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/745 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/745' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721678 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 Building ZINC000180721678 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721678 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 742) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 743) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 744) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 745) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721678 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 Building ZINC000180721678 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721678 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 742) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 743) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 744) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 745) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721678 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 Building ZINC000180721678 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721678 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 742) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/742: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 743) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 744) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 13, 20, 14, 20, 34, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 20, 20, 13, 20, 33, 33, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 745) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@H](O)C2)cc1) `ZINC000180721678.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721678 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 13, 20, 20, 15, 20, 12, 20, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 20, 20, 13, 20, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 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, 46, 47, 48, 49, 50]) total number of confs: 384 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721678 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721678 Building ZINC000180721698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/746 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/747 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/748 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/748' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/749 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/749' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 Building ZINC000180721698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 746) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 747) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 748) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 749) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 Building ZINC000180721698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 746) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 747) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 748) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 749) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 Building ZINC000180721698 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180721698 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 746) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 747) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 748) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 14, 21, 21, 14, 21, 14, 21, 39, 50, 50, 50, 50, 50, 50, 5, 5, 5, 5, 5, 5, 5, 3, 14, 14, 21, 21, 14, 21, 36, 36, 50, 50, 50, 50, 150, 50, 50, 5, 5] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 749) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/749: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NCc2ccccc2CN2CC[C@@H](O)C2)cc1) `ZINC000180721698.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180721698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000180721698 none COc1ccc([C@]([O-])([SiH3])C(=O)NCc2ccccc2CN2CC[C@@H](O)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 7, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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, 7, 7, 7] 1 hydrogens 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, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 13, 19, 19, 19, 19, 14, 19, 33, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 19, 19, 19, 19, 32, 32, 50, 50, 50, 50, 150, 50, 50, 4, 4] 150 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, 46, 47, 48, 49, 50]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180721698 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180721698 Building ZINC000181362528 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181362528 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/750 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1) `ZINC000181362528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181362528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000181362528 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 7, 8, 8, 8, 15, 15, 15, 24, 5, 5, 18, 18, 18, 18, 18, 5, 6, 8, 8, 8, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/751 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1) `ZINC000181362528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181362528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000181362528 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 22, 5, 5, 18, 18, 18, 18, 18, 5, 6, 8, 8, 8, 22, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000181362528 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 Building ZINC000181362528 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181362528 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 750) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/750: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1) `ZINC000181362528.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181362528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000181362528 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 7, 8, 8, 8, 15, 15, 15, 24, 5, 5, 18, 18, 18, 18, 18, 5, 6, 8, 8, 8, 24, 24, 24, 24, 24, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 751) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1) `ZINC000181362528.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181362528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000181362528 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2c(F)cccc2S(=O)(=O)CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 15, 1, 1, 1, 1, 14, 11, 11, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 15, 15, 15, 22, 5, 5, 18, 18, 18, 18, 18, 5, 6, 8, 8, 8, 22, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000181362528 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181362528 Building ZINC000466530005 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466530005 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/752 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466530005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530005 none CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 7, 11, 3, 7, 7, 15, 24, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 15, 15, 24, 24, 24, 24, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/753 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466530005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530005 none CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 2, 6, 6, 12, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 12, 12, 21, 21, 21, 21, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466530005 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 Building ZINC000466530005 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466530005 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 752) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530005.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466530005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530005 none CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 7, 11, 3, 7, 7, 15, 24, 24, 24, 24, 24, 24, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 15, 15, 24, 24, 24, 24, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 753) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/753: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530005.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466530005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530005 none CCOC(=O)[C@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 2, 6, 6, 12, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 12, 12, 21, 21, 21, 21, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530005 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466530005 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530005 Building ZINC000466530006 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466530006 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/754 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466530006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530006 none CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 2, 6, 6, 12, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 12, 12, 21, 21, 21, 21, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/755 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466530006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530006 none CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 7, 11, 3, 7, 7, 14, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 14, 14, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466530006 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 Building ZINC000466530006 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466530006 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 754) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/754: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466530006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530006 none CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 10, 2, 6, 6, 12, 21, 21, 21, 21, 21, 21, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 12, 12, 21, 21, 21, 21, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 755) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/755: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000466530006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466530006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000466530006 none CCOC(=O)[C@@H](Cc1cccc(Cl)c1)NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 1, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 7, 11, 3, 7, 7, 14, 23, 23, 23, 23, 23, 23, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 14, 14, 23, 23, 23, 23, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466530006 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466530006 Building ZINC000181817102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181817102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/756 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1) `ZINC000181817102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181817102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181817102 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 7, 26, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/757 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1) `ZINC000181817102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181817102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181817102 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 11, 7, 25, 25, 25, 25, 25, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000181817102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 Building ZINC000181817102 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181817102 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 756) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/756: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1) `ZINC000181817102.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181817102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181817102 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 1, 1, 10, 10, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 10, 7, 26, 26, 26, 26, 26, 10, 10] 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 757) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/757: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1) `ZINC000181817102.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181817102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181817102 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cn(C)cc(Br)c2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'Br', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 8, 5, 1, 1, 17, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 11, 11, 11, 7, 25, 25, 25, 25, 25, 11, 11] 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]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000181817102 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000181817102 Building ZINC000117983791 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117983791 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/758 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/758' -> `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)NCCc1csc(N2CCCC2)n1) `ZINC000117983791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117983791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000117983791 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)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.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 14, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 27, 43, 43, 43, 43, 45, 45, 45, 45, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 27, 27, 43, 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]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/759 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/759' -> `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)NCCc1csc(N2CCCC2)n1) `ZINC000117983791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117983791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000117983791 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)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.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 14, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 26, 43, 43, 43, 43, 45, 45, 45, 45, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 26, 26, 43, 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]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000117983791 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 Building ZINC000117983791 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000117983791 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 758) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/758: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)n1) `ZINC000117983791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000117983791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000117983791 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)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.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 14, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 27, 43, 43, 43, 43, 45, 45, 45, 45, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 27, 27, 43, 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]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 759) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/759: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)n1) `ZINC000117983791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000117983791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000117983791 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1csc(N2CCCC2)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.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 14, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 26, 43, 43, 43, 43, 45, 45, 45, 45, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 26, 26, 43, 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]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000117983791 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000117983791 Building ZINC001350785990 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350785990 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/760 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br) `ZINC001350785990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350785990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350785990 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 31, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 49, 49, 49, 49] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/761 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br) `ZINC001350785990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350785990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350785990 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 30, 30, 49, 49, 49, 49] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350785990 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 Building ZINC001350785990 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350785990 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 760) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/760: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br) `ZINC001350785990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350785990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350785990 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 31, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 31, 31, 49, 49, 49, 49] 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 761) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/761: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br) `ZINC001350785990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350785990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001350785990 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncn(C)c1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 18, 30, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 30, 30, 49, 49, 49, 49] 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350785990 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350785990 Building ZINC000183732854 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183732854 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/762 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/763 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/764 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/764' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/765 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/765' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732854 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 Building ZINC000183732854 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183732854 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 762) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 763) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 764) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 765) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732854 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 Building ZINC000183732854 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183732854 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 762) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 763) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 764) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 765) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732854 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 Building ZINC000183732854 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183732854 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 762) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/762: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 763) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/763: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 10, 16, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 50, 21, 21, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 21, 21] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 764) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/764: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 765) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/765: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1) `ZINC000183732854.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183732854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732854 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(c2ccc(C)nn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 5, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 9, 17, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22, 2, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 50, 50, 50, 50, 50, 22, 22, 22, 22] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732854 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732854 Building ZINC000183732935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183732935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/766 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1) `ZINC000183732935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732935 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 16, 16, 46, 46, 46, 46, 46, 4, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 16, 16, 16, 46, 46, 46, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/767 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1) `ZINC000183732935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732935 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 20, 20, 48, 48, 48, 48, 48, 5, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 20, 20, 20, 48, 48, 48, 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]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 Building ZINC000183732935 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183732935 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 766) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/766: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1) `ZINC000183732935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183732935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732935 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 16, 16, 46, 46, 46, 46, 46, 4, 4, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 16, 16, 16, 46, 46, 46, 4, 4, 4, 4] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 83 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 767) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/767: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1) `ZINC000183732935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183732935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183732935 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCC(N(C)c2cccnn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 1, 1, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 20, 20, 48, 48, 48, 48, 48, 5, 5, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 20, 20, 20, 48, 48, 48, 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]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183732935 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183732935 Building ZINC000183733002 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733002 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/768 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1) `ZINC000183733002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733002 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 27, 48, 48, 48, 50, 50, 48, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 27, 27, 144, 50, 50, 48, 50, 50, 14, 14, 14, 14] 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: 352 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/769 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1) `ZINC000183733002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733002 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 27, 42, 42, 42, 47, 47, 42, 47, 47, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 27, 27, 126, 47, 47, 42, 47, 47, 13, 13, 13, 13] 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: 323 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733002 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 Building ZINC000183733002 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733002 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 768) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/768: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1) `ZINC000183733002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733002 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 14, 14, 14, 14, 27, 48, 48, 48, 50, 50, 48, 50, 50, 14, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 27, 27, 144, 50, 50, 48, 50, 50, 14, 14, 14, 14] 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: 352 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 769) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1) `ZINC000183733002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733002 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 27, 42, 42, 42, 47, 47, 42, 47, 47, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 27, 27, 126, 47, 47, 42, 47, 47, 13, 13, 13, 13] 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: 323 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733002 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733002 Building ZINC000183733023 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733023 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/770 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1) `ZINC000183733023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733023 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 24, 46, 46, 46, 48, 48, 46, 48, 48, 11, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 24, 24, 138, 48, 48, 46, 48, 48, 11, 11, 11, 11] 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: 349 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/771 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1) `ZINC000183733023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733023 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 14, 26, 44, 44, 44, 47, 47, 44, 47, 47, 14, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 26, 26, 132, 47, 47, 44, 47, 47, 14, 14, 14, 14] 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: 322 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733023 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 Building ZINC000183733023 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183733023 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 770) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1) `ZINC000183733023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733023 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 4, 4, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 24, 46, 46, 46, 48, 48, 46, 48, 48, 11, 11, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 24, 24, 138, 48, 48, 46, 48, 48, 11, 11, 11, 11] 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: 349 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 771) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1) `ZINC000183733023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733023 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(C[C@@H](O)c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 14, 14, 14, 14, 26, 44, 44, 44, 47, 47, 44, 47, 47, 14, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 26, 26, 132, 47, 47, 44, 47, 47, 14, 14, 14, 14] 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: 322 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733023 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733023 Building ZINC000183733225 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733225 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/772 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/773 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/774 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/774' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/775 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/775' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733225 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 Building ZINC000183733225 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733225 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 772) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 773) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 774) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 775) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733225 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 Building ZINC000183733225 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733225 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 772) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 773) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 774) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 775) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733225 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 Building ZINC000183733225 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733225 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 772) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 773) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/773: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 14, 27, 50, 50, 50, 50, 50, 14, 14, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 774) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/774: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 775) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/775: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1) `ZINC000183733225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183733225 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCCN(Cc2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 25, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 25, 25, 50, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733225 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733225 Building ZINC000183733246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/776 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/777 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/778 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/778' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/779 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/779' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 Building ZINC000183733246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 776) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 777) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 778) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 779) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 Building ZINC000183733246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 776) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 777) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 778) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 779) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 Building ZINC000183733246 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183733246 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 776) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 777) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 8, 8, 4, 1, 5, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 34, 34, 50, 50, 50, 50, 50, 34, 17, 17, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 778) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/778: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 779) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/779: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1) `ZINC000183733246.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183733246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183733246 none CCn1cc(CN2CCCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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, 8, 1, 1, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 8, 8, 8, 8, 8, 4, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 32, 16, 16, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 32] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183733246 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183733246 Building ZINC000183745644 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745644 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/780 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1) `ZINC000183745644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 12, 12, 12, 12, 24, 24, 24, 48, 48, 48, 48, 48, 12, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 24, 24, 24, 48, 48, 48, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/781 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1) `ZINC000183745644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 23, 23, 23, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 23, 23, 23, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745644 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 Building ZINC000183745644 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745644 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 780) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1) `ZINC000183745644.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745644 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 12, 12, 12, 12, 24, 24, 24, 48, 48, 48, 48, 48, 12, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 24, 24, 24, 48, 48, 48, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 781) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1) `ZINC000183745644.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745644 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 23, 23, 23, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 23, 23, 23, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 121 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745644 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745644 Building ZINC000183745662 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745662 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/782 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1) `ZINC000183745662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745662 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 25, 25, 25, 48, 48, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 25, 25, 25, 48, 48, 48, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/783 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1) `ZINC000183745662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745662 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 27, 27, 27, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 27, 27, 27, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745662 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 Building ZINC000183745662 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745662 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 782) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1) `ZINC000183745662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745662 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 10, 10, 10, 10, 25, 25, 25, 48, 48, 48, 48, 48, 10, 10, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 25, 25, 25, 48, 48, 48, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 127 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 783) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/783: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1) `ZINC000183745662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745662 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN([C@@H](C)c2nc(C)no2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 7, 5, 1, 8, 1, 5, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 5, 11, 11, 11, 11, 27, 27, 27, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 27, 27, 27, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745662 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745662 Building ZINC000183745761 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745761 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/784 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1) `ZINC000183745761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745761 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 29, 48, 48, 48, 48, 48, 48, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 29, 29, 48, 48, 48, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/785 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1) `ZINC000183745761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745761 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 8, 12, 12, 12, 12, 12, 12, 28, 49, 49, 49, 49, 49, 49, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 28, 28, 49, 49, 49, 49, 49, 49, 49, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745761 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 Building ZINC000183745761 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745761 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 784) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1) `ZINC000183745761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745761 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 7, 13, 13, 13, 13, 13, 13, 29, 48, 48, 48, 48, 48, 48, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 29, 29, 48, 48, 48, 48, 48, 48, 48, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 785) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1) `ZINC000183745761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745761 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 8, 12, 12, 12, 12, 12, 12, 28, 49, 49, 49, 49, 49, 49, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 28, 28, 49, 49, 49, 49, 49, 49, 49, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745761 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745761 Building ZINC000183745779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/786 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1) `ZINC000183745779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745779 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 26, 46, 46, 46, 46, 46, 46, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 26, 26, 46, 46, 46, 46, 46, 46, 46, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/787 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1) `ZINC000183745779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745779 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 28, 44, 44, 44, 44, 44, 44, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 28, 28, 44, 44, 44, 44, 44, 44, 44, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 Building ZINC000183745779 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745779 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 786) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1) `ZINC000183745779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745779 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 12, 12, 26, 46, 46, 46, 46, 46, 46, 12, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 26, 26, 46, 46, 46, 46, 46, 46, 46, 12, 12] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 787) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/787: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1) `ZINC000183745779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000183745779 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCO[C@@H](Cn2nc(C)cc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 5, 8, 8, 1, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 28, 44, 44, 44, 44, 44, 44, 10, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 28, 28, 44, 44, 44, 44, 44, 44, 44, 10, 10] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745779 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745779 Building ZINC000183745994 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745994 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/788 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1) `ZINC000183745994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183745994 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 23, 46, 46, 46, 46, 46, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 23, 23, 46, 46, 46, 46, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/789 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1) `ZINC000183745994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183745994 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 26, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745994 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 Building ZINC000183745994 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745994 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 788) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/788: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1) `ZINC000183745994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183745994 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 23, 46, 46, 46, 46, 46, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 23, 23, 46, 46, 46, 46, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 789) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1) `ZINC000183745994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000183745994 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2cnc(C)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 8, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 2, 4, 11, 11, 11, 11, 26, 50, 50, 50, 50, 50, 11, 11, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 26, 26, 50, 50, 50, 50, 11, 11, 11, 11] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183745994 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183745994 Building ZINC000183882231 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183882231 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/790 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1) `ZINC000183882231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183882231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183882231 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 26, 46, 46, 46, 46, 46, 46, 46, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/791 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1) `ZINC000183882231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183882231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183882231 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 27, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183882231 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 Building ZINC000183882231 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183882231 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 790) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1) `ZINC000183882231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183882231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183882231 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 26, 46, 46, 46, 46, 46, 46, 46, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 26, 26, 46, 46, 46, 46, 46, 46, 46, 46, 46, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 791) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1) `ZINC000183882231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183882231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000183882231 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCN(Cc2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 6, 13, 13, 13, 13, 27, 50, 50, 50, 50, 50, 50, 50, 13, 13, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183882231 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183882231 Building ZINC000183948491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183948491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/792 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/793 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/794 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/794' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/795 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/795' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183948491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 Building ZINC000183948491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183948491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 792) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 793) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 794) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 795) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183948491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 Building ZINC000183948491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183948491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 792) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 793) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 794) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 795) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183948491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 Building ZINC000183948491 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000183948491 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 792) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 793) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 288 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 794) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 795) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000183948491.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000183948491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000183948491 none CCN(CCO)CCNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 13, 23, 31, 31, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 13, 13, 10, 10, 2, 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, 49, 50, 51]) total number of confs: 282 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000183948491 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000183948491 Building ZINC000184037367 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000184037367 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/796 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/797 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/798 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/798' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/799 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/799' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184037367 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 Building ZINC000184037367 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000184037367 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 796) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 797) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 798) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 799) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184037367 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 Building ZINC000184037367 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000184037367 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 796) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 797) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 798) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 799) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184037367 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 Building ZINC000184037367 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000184037367 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 796) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 797) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 798) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 16, 20, 20, 20, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 6, 16, 16, 60, 26, 26, 48, 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: 221 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 799) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/799: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1) `ZINC000184037367.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000184037367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000184037367 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H](O)CN1CCc2ccccc2C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 11, 17, 17, 17, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 11, 11, 51, 26, 26, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 218 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184037367 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184037367 Building ZINC000184150348 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184150348 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/800 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1) `ZINC000184150348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184150348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000184150348 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 20, 6, 20, 20, 20, 20, 20, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/801 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1) `ZINC000184150348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184150348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000184150348 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 21, 21, 21, 7, 21, 21, 21, 21, 21, 7, 7, 2, 2, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 21, 21, 21, 7, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184150348 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 Building ZINC000184150348 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184150348 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 800) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/800: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1) `ZINC000184150348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184150348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000184150348 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 2, 2, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 20, 20, 20, 6, 20, 20, 20, 20, 20, 6, 6, 2, 2, 5, 5, 5, 5, 5, 2, 6, 6, 6, 6, 20, 20, 20, 11, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 801) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/801: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1) `ZINC000184150348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184150348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000184150348 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(c3nc(C)cc(C(C)C)n3)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 8, 1, 5, 1, 1, 5, 5, 5, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 2, 2, 1, 1, 1, 1, 2, 6, 7, 7, 7, 7, 21, 21, 21, 7, 21, 21, 21, 21, 21, 7, 7, 2, 2, 4, 4, 4, 4, 4, 2, 7, 7, 7, 7, 21, 21, 21, 7, 21, 21, 21, 21, 21, 21, 21, 7, 7, 7, 7, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184150348 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184150348 Building ZINC000184137326 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184137326 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/802 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)n1) `ZINC000184137326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184137326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000184137326 none Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 28, 28, 29, 29, 28, 9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 28, 28, 28, 28, 16, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 2, 2, 2, 2, 2, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/803 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)n1) `ZINC000184137326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184137326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000184137326 none Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 31, 31, 30, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184137326 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 Building ZINC000184137326 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184137326 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 802) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/802: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)n1) `ZINC000184137326.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184137326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000184137326 none Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 16, 28, 28, 29, 29, 28, 9, 9, 9, 9, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 28, 28, 28, 28, 16, 29, 29, 29, 29, 29, 29, 29, 9, 9, 9, 9, 2, 2, 2, 2, 2, 9, 9, 9, 9] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 803) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/803: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)n1) `ZINC000184137326.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184137326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000184137326 none Cc1cc(C(C)C)nc(N2CCN(C(=O)[C@]([O-])([SiH3])c3cnn(C)c3)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 5, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 31, 31, 30, 8, 8, 8, 8, 5, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 30, 30, 30, 30, 30, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8] 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, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000184137326 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000184137326 Building ZINC001526573472 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526573472 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/804 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1) `ZINC001526573472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526573472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001526573472 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 22, 22, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/805 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1) `ZINC001526573472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526573472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001526573472 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526573472 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 Building ZINC001526573472 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526573472 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 804) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/804: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1) `ZINC001526573472.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526573472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001526573472 none CC(C)C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 22, 22, 31, 31, 31, 31, 31, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 805) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/805: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1) `ZINC001526573472.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526573472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001526573472 none CC(C)C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 18, 18, 27, 27, 27, 27, 27, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 105 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526573472 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526573472 Building ZINC000466755480 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755480 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/806 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755480 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 7, 3, 7, 7, 15, 20, 25, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 17, 17, 20, 19, 25, 25, 25, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/807 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755480 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 6, 2, 6, 6, 15, 19, 27, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 17, 17, 19, 17, 27, 27, 27, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755480 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 Building ZINC000466755480 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755480 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 806) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/806: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755480.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755480 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 7, 3, 7, 7, 15, 20, 25, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 17, 17, 20, 19, 25, 25, 25, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 807) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755480.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755480 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 6, 2, 6, 6, 15, 19, 27, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 17, 17, 19, 17, 27, 27, 27, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755480 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755480 Building ZINC000466755425 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755425 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/808 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755425 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 2, 8, 8, 20, 28, 41, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 22, 22, 22, 22, 23, 23, 28, 27, 41, 41, 41, 2, 2, 2, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/809 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755425 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 8, 10, 3, 8, 8, 20, 25, 39, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 22, 22, 25, 24, 39, 39, 39, 3, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755425 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 Building ZINC000466755425 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755425 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 808) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755425 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 2, 8, 8, 20, 28, 41, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 22, 22, 22, 22, 22, 23, 23, 28, 27, 41, 41, 41, 2, 2, 2, 2, 2] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 809) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/809: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755425 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 10, 8, 10, 3, 8, 8, 20, 25, 39, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 24, 24, 24, 24, 24, 22, 22, 25, 24, 39, 39, 39, 3, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755425 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755425 Building ZINC000466755426 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755426 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/810 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755426 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 7, 9, 3, 7, 7, 19, 24, 39, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 21, 21, 24, 23, 39, 39, 39, 3, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/811 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755426 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 2, 8, 8, 20, 28, 41, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 22, 22, 22, 22, 22, 23, 23, 28, 27, 41, 41, 41, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755426 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 Building ZINC000466755426 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755426 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 810) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/810: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755426 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 7, 9, 3, 7, 7, 19, 24, 39, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 23, 23, 23, 23, 23, 21, 21, 24, 23, 39, 39, 39, 3, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 811) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/811: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000466755426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000466755426 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 11, 8, 11, 2, 8, 8, 20, 28, 41, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 22, 22, 22, 22, 22, 23, 23, 28, 27, 41, 41, 41, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755426 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755426 Building ZINC000466755479 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755479 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/812 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755479 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 6, 2, 6, 6, 15, 19, 27, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 17, 17, 17, 19, 27, 27, 27, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/813 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/813' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755479 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 7, 3, 7, 7, 15, 20, 25, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 17, 17, 19, 20, 25, 25, 25, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755479 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 Building ZINC000466755479 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466755479 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 812) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/812: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466755479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755479 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 6, 6, 6, 6, 2, 6, 6, 15, 19, 27, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 17, 17, 17, 19, 27, 27, 27, 2, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 813) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/813: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000466755479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466755479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000466755479 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 7, 7, 7, 3, 7, 7, 15, 20, 25, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 17, 17, 19, 20, 25, 25, 25, 3, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466755479 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466755479 Building ZINC000185965612 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185965612 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/814 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185965612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965612 none CCc1noc([C@@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 33, 33, 33, 16, 9, 16, 16, 9, 9, 9, 5, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 9, 9, 33, 48, 48, 48, 48, 48, 16, 16, 16, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/815 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185965612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965612 none CCc1noc([C@@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 21, 8, 21, 21, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 38, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000185965612 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 Building ZINC000185965612 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185965612 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 814) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/814: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185965612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965612 none CCc1noc([C@@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 33, 33, 33, 33, 16, 9, 16, 16, 9, 9, 9, 5, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 9, 9, 33, 48, 48, 48, 48, 48, 16, 16, 16, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 815) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/815: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185965612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965612 none CCc1noc([C@@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 21, 8, 21, 21, 8, 8, 8, 4, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 8, 8, 38, 50, 50, 50, 50, 50, 21, 21, 21, 8, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 172 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000185965612 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965612 Building ZINC000185965630 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185965630 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/816 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185965630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965630 none CCc1noc([C@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 33, 33, 33, 16, 7, 16, 16, 7, 7, 7, 4, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 7, 7, 33, 46, 46, 46, 46, 46, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 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, 50]) total number of confs: 154 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/817 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185965630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965630 none CCc1noc([C@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 19, 6, 19, 19, 6, 6, 6, 3, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 6, 6, 39, 50, 50, 50, 50, 50, 19, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 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, 50]) total number of confs: 166 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000185965630 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 Building ZINC000185965630 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185965630 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 816) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/816: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185965630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965630 none CCc1noc([C@H](C)N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 33, 33, 33, 16, 7, 16, 16, 7, 7, 7, 4, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 7, 7, 33, 46, 46, 46, 46, 46, 16, 16, 16, 7, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 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, 50]) total number of confs: 154 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 817) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1noc([C@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1) `ZINC000185965630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185965630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000185965630 none CCc1noc([C@H](C)N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3OC)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 19, 6, 19, 19, 6, 6, 6, 3, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 6, 6, 39, 50, 50, 50, 50, 50, 19, 19, 19, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 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, 50]) total number of confs: 166 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000185965630 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000185965630 Building ZINC000186022573 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022573 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/818 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/819 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/820 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/820' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/821 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/821' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022573 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 Building ZINC000186022573 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022573 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 818) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 819) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 820) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 821) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022573 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 Building ZINC000186022573 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022573 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 818) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 819) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 820) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 821) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022573 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 Building ZINC000186022573 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022573 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 818) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 819) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/819: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 24, 24, 24, 24, 24, 24, 49, 49, 49, 49, 49, 24, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 24, 24, 24, 24, 24, 24, 49, 49, 49, 24, 24] 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: 96 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 820) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/820: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 821) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1) `ZINC000186022573.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022573 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 7, 11, 25, 25, 25, 25, 25, 25, 49, 49, 49, 49, 49, 25, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 25, 25, 25, 25, 25, 25, 49, 49, 49, 25, 25] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022573 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022573 Building ZINC000186022594 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022594 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/822 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/823 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/824 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/824' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/825 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/825' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022594 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 Building ZINC000186022594 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022594 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 822) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 823) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 824) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 825) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022594 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 Building ZINC000186022594 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022594 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 822) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 823) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 824) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 825) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022594 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 Building ZINC000186022594 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186022594 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 822) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 823) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/823: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 10, 28, 28, 28, 28, 28, 28, 49, 49, 49, 49, 49, 28, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 28, 28, 28, 28, 28, 28, 49, 49, 49, 28, 28] 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: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 824) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/824: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 825) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/825: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1) `ZINC000186022594.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186022594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000186022594 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)[C@H]1CCCN(c2cccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 27, 27, 27, 27, 27, 27, 49, 49, 49, 49, 49, 27, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 27, 27, 27, 27, 27, 27, 49, 49, 49, 27, 27] 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: 105 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186022594 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186022594 Building ZINC000186667838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/826 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/827 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/828 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/828' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/829 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/829' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 Building ZINC000186667838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 826) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 827) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 828) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 829) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 Building ZINC000186667838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 826) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 827) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 828) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 829) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 Building ZINC000186667838 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667838 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 826) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 827) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 23, 26, 26, 26, 12, 12, 12, 12, 12, 8, 2, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 12, 12, 23, 23, 23, 26, 26, 78, 12, 12, 12, 12, 12, 12, 3, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12] 150 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 181 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 828) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/828: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 829) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/829: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667838.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667838 none CN(CC(=O)O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 23, 26, 26, 26, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 2, 2, 4, 4, 2, 4, 4, 4, 13, 13, 23, 23, 23, 26, 26, 78, 13, 13, 13, 13, 13, 13, 2, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 13] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667838 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667838 Building ZINC000186667860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/830 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/831 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/832 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/832' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/833 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/833' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 Building ZINC000186667860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 830) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 831) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 832) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 833) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 Building ZINC000186667860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 830) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 831) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 832) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 833) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 Building ZINC000186667860 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000186667860 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 830) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/830: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 831) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/831: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 10, 22, 24, 26, 26, 10, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 8, 8, 6, 8, 8, 8, 10, 10, 22, 22, 22, 24, 24, 78, 10, 10, 10, 10, 10, 10, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 832) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 833) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1) `ZINC000186667860.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000186667860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000186667860 none CN(CC(=O)O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 1, 11, 12, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 23, 27, 27, 27, 11, 11, 11, 11, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 23, 23, 23, 27, 27, 81, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 168 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186667860 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186667860 Building ZINC000186888435 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186888435 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/834 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1) `ZINC000186888435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186888435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186888435 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 5, 5, 8, 8, 6, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 1, 1, 2, 6, 8, 11, 11, 11, 11, 40, 40, 40, 50, 50, 40, 40, 40, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/835 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1) `ZINC000186888435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186888435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186888435 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 5, 5, 8, 8, 6, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 39, 39, 39, 50, 50, 39, 39, 39, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186888435 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 Building ZINC000186888435 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000186888435 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 834) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1) `ZINC000186888435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000186888435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186888435 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 5, 5, 8, 8, 6, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 2, 1, 1, 1, 2, 6, 8, 11, 11, 11, 11, 40, 40, 40, 50, 50, 40, 40, 40, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 40, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 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, 46, 47]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 835) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/835: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1) `ZINC000186888435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000186888435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000186888435 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(c3cc(C4CC4)n[nH]3)CC2)cc1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 5, 5, 5, 8, 8, 6, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 39, 39, 39, 50, 50, 39, 39, 39, 8, 8, 2, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 39, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000186888435 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000186888435 Building ZINC000466774679 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466774679 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/836 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466774679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774679 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 6, 6, 10, 12, 17, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/837 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466774679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774679 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 4, 2, 4, 4, 10, 12, 18, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 12, 12, 18, 18, 18, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466774679 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 Building ZINC000466774679 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466774679 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 836) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/836: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774679.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466774679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774679 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 6, 6, 10, 12, 17, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 837) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/837: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774679.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466774679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774679 none CCOC(=O)[C@@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 4, 2, 4, 4, 10, 12, 18, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 12, 12, 18, 18, 18, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466774679 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774679 Building ZINC000466774680 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466774680 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/838 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466774680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774680 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 4, 2, 4, 4, 10, 12, 18, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 12, 12, 18, 18, 18, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/839 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466774680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774680 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 6, 6, 10, 12, 17, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466774680 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 Building ZINC000466774680 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000466774680 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 838) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000466774680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774680 none CCOC(=O)[C@H](CCOC)NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 4, 2, 4, 4, 10, 12, 18, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 12, 12, 18, 18, 18, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 839) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1) `ZINC000466774680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000466774680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000466774680 none CCOC(=O)[C@H](CCOC)NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 6, 2, 6, 6, 10, 12, 17, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 2, 4, 4, 9, 9, 9, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000466774680 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000466774680 Building ZINC000794334081 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000794334081 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/840 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)cn1) `ZINC000794334081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000794334081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000794334081 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 3, 3, 4, 10, 13, 4, 7, 12, 12, 12, 12, 12, 12, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 10, 10, 13, 13, 39, 7, 7, 12, 12, 12, 4] 150 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]) total number of confs: 155 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/841 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)cn1) `ZINC000794334081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000794334081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000794334081 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7] 1 hydrogens 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, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 4, 10, 13, 4, 7, 12, 12, 12, 12, 12, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 13, 13, 39, 7, 7, 12, 12, 12, 5] 150 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]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000794334081 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 Building ZINC000794334081 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000794334081 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 840) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/840: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)cn1) `ZINC000794334081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000794334081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000794334081 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 3, 3, 4, 10, 13, 4, 7, 12, 12, 12, 12, 12, 12, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 10, 10, 13, 13, 39, 7, 7, 12, 12, 12, 4] 150 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]) total number of confs: 155 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 841) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/841: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)cn1) `ZINC000794334081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000794334081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000794334081 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N(CCO)Cc2cccnc2Cl)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', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 1, 1, 1, 1, 8, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 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, 7, 7] 1 hydrogens 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, 5, 10, 10, 5, 5, 1, 1, 1, 1, 3, 3, 4, 10, 13, 4, 7, 12, 12, 12, 12, 12, 12, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 10, 10, 13, 13, 39, 7, 7, 12, 12, 12, 5] 150 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]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000794334081 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000794334081 Building ZINC000188449052 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188449052 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/842 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)cn1) `ZINC000188449052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188449052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000188449052 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', '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, 15, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 14, 14, 28, 28, 28, 7, 7, 7, 7, 7, 7, 2, 14, 14, 28, 28, 7] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/843 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)cn1) `ZINC000188449052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188449052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000188449052 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', '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, 15, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 14, 14, 28, 28, 28, 7, 7, 7, 7, 7, 7, 2, 14, 14, 28, 28, 7] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188449052 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 Building ZINC000188449052 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188449052 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 842) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/842: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)cn1) `ZINC000188449052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188449052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000188449052 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', '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, 15, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 14, 14, 28, 28, 28, 7, 7, 7, 7, 7, 7, 2, 14, 14, 28, 28, 7] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 843) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)cn1) `ZINC000188449052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188449052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000188449052 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2c(F)cc(Br)cc2F)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', 'F', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', '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, 15, 1, 1, 17, 1, 1, 15, 1, 8, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 14, 14, 28, 28, 28, 7, 7, 7, 7, 7, 7, 2, 14, 14, 28, 28, 7] 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]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188449052 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188449052 Building ZINC000188508580 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188508580 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/844 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1) `ZINC000188508580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188508580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000188508580 none O=C(NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 30, 29, 30, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/845 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1) `ZINC000188508580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188508580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000188508580 none O=C(NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 17, 35, 35, 35, 11, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188508580 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 Building ZINC000188508580 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188508580 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 844) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1) `ZINC000188508580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188508580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000188508580 none O=C(NC1CN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 30, 29, 30, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 845) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/845: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1) `ZINC000188508580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188508580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000188508580 none O=C(NC1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1)C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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] 0 hydrogens 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, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 17, 35, 35, 35, 11, 4, 4, 4, 4, 5, 5, 4, 5, 5, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188508580 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188508580 Building ZINC000188647551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000188647551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/846 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/846' -> `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]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/847 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/847' -> `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]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 15, 15, 15, 15, 15, 15, 42, 45, 45, 45, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/848 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/848' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/849 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/849' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 42, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188647551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 Building ZINC000188647551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000188647551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 846) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 847) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 15, 15, 15, 15, 15, 15, 42, 45, 45, 45, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 848) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 849) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 42, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188647551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 Building ZINC000188647551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000188647551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 846) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 847) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 15, 15, 15, 15, 15, 15, 42, 45, 45, 45, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 848) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 849) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 42, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188647551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 Building ZINC000188647551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000188647551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 846) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/846: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 847) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/847: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 15, 15, 15, 15, 15, 15, 42, 45, 45, 45, 45, 45, 15, 15, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 15, 45, 45, 45, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 848) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/848: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 43, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 849) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/849: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)CC1) `ZINC000188647551.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000188647551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000188647551 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](Oc2cnccn2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 1, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 6, 16, 16, 16, 16, 16, 16, 42, 46, 46, 46, 46, 46, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188647551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188647551 Building ZINC000188925251 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188925251 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/850 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/850' -> `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)N1CCCNC(=O)[C@H]1C) `ZINC000188925251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188925251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000188925251 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/851 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/851' -> `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)N1CCCNC(=O)[C@H]1C) `ZINC000188925251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188925251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000188925251 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188925251 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 Building ZINC000188925251 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000188925251 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 850) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C) `ZINC000188925251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000188925251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000188925251 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 15, 15, 5, 15, 15, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 851) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C) `ZINC000188925251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000188925251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000188925251 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCNC(=O)[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 2, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 7, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 79 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000188925251 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000188925251 Building ZINC000189230300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189230300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/852 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1) `ZINC000189230300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189230300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189230300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1 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', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 21, 31, 33, 46, 46, 46, 46, 46, 46, 46, 45, 46, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 31, 31, 46, 46, 46, 46, 46, 46, 46, 46, 6, 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: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/853 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1) `ZINC000189230300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189230300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189230300 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1 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', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 19, 29, 31, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 5, 19, 19, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 6, 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: 235 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189230300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 Building ZINC000189230300 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189230300 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 852) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/852: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1) `ZINC000189230300.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189230300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189230300 none COc1ccc([C@@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1 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', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 21, 31, 33, 46, 46, 46, 46, 46, 46, 46, 45, 46, 6, 6, 6, 6, 6, 6, 6, 5, 21, 21, 31, 31, 46, 46, 46, 46, 46, 46, 46, 46, 6, 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: 232 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 853) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/853: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1) `ZINC000189230300.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189230300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC000189230300 none COc1ccc([C@]([O-])([SiH3])C(=O)NCCN2CCc3ccccc3C2=O)cc1 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', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 5, 5, 5, 19, 29, 31, 46, 46, 46, 46, 46, 46, 46, 46, 46, 6, 6, 6, 6, 6, 6, 6, 5, 19, 19, 29, 29, 46, 46, 46, 46, 46, 46, 46, 46, 6, 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: 235 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189230300 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189230300 Building ZINC000189416381 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189416381 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/854 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/854' -> `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)N1CC(NC(=O)C2CC2)C1) `ZINC000189416381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189416381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000189416381 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 32, 32, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 3, 3, 3, 11, 32, 32, 32, 32, 32, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/855 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/855' -> `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)N1CC(NC(=O)C2CC2)C1) `ZINC000189416381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189416381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000189416381 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 14, 14, 14, 31, 31, 5, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 5, 5, 5, 14, 31, 31, 31, 31, 31, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189416381 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 Building ZINC000189416381 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189416381 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 854) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1) `ZINC000189416381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189416381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000189416381 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 32, 32, 3, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 3, 3, 3, 11, 32, 32, 32, 32, 32, 3, 3] 50 rigid atoms, others: [12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 109 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 855) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1) `ZINC000189416381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189416381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000189416381 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 5, 14, 14, 14, 31, 31, 5, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 5, 5, 5, 14, 31, 31, 31, 31, 31, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189416381 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189416381 Building ZINC000189930602 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189930602 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/856 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1) `ZINC000189930602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189930602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000189930602 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/857 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/857' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1) `ZINC000189930602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189930602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000189930602 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189930602 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 Building ZINC000189930602 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000189930602 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 856) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1) `ZINC000189930602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000189930602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000189930602 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 857) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1) `ZINC000189930602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000189930602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000189930602 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)nc(N(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.ar', 'C.ar', 'N.pl3', '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'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000189930602 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000189930602 Building ZINC000381444961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000381444961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/858 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1) `ZINC000381444961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000381444961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000381444961 none O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 17, 1, 6, 6, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 27, 12, 34, 34] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/859 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1) `ZINC000381444961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000381444961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000381444961 none O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 17, 1, 6, 6, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 27, 12, 34, 34] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000381444961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 Building ZINC000381444961 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000381444961 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 858) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1) `ZINC000381444961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000381444961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000381444961 none O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 17, 1, 6, 6, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 27, 12, 34, 34] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 859) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1) `ZINC000381444961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000381444961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 23 natoms 22 natoms 21 natoms 20 names: ZINC000381444961 none O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cnc(Br)c(Br)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Br', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 8, 1, 17, 1, 17, 1, 6, 6, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 1, 1, 1, 12, 12, 12, 34, 34, 34, 34, 34, 34, 34, 27, 12, 34, 34] 150 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000381444961 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381444961 Building ZINC000381505934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000381505934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/860 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl) `ZINC000381505934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000381505934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 24 natoms 23 natoms 22 natoms 21 names: ZINC000381505934 none O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 1, 16, 6, 6, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 12, 12, 12, 34, 34, 34, 26, 34, 34, 34, 21, 12, 34, 24, 34] 147 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/861 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl) `ZINC000381505934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000381505934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 24 natoms 23 natoms 22 natoms 21 names: ZINC000381505934 none O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 1, 16, 6, 6, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 12, 12, 12, 34, 34, 34, 26, 34, 34, 34, 21, 12, 34, 30, 34] 147 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000381505934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 Building ZINC000381505934 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000381505934 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 860) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/860: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl) `ZINC000381505934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000381505934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 24 natoms 23 natoms 22 natoms 21 names: ZINC000381505934 none O=C(O)[C@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 1, 16, 6, 6, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 12, 12, 12, 34, 34, 34, 26, 34, 34, 34, 21, 12, 34, 24, 34] 147 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 861) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/861: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl) `ZINC000381505934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000381505934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 24 natoms 23 natoms 22 natoms 21 names: ZINC000381505934 none O=C(O)[C@@]([O-])([SiH3])C(=O)Nc1cc(I)ccc1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'O.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 12, 5, 12, 1, 11, 8, 1, 1, 1, 18, 1, 1, 1, 16, 6, 6, 7, 7, 7] dock color type numbers: [5, 9, 4, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 12, 12, 12, 34, 34, 34, 26, 34, 34, 34, 21, 12, 34, 30, 34] 147 rigid atoms, others: [1, 3, 4, 5] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000381505934 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000381505934 Building ZINC000119081421 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119081421 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/862 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1) `ZINC000119081421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119081421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081421 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 31, 32, 39, 31, 31, 31, 31, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 13, 13, 32, 32, 39, 39, 117, 31, 31, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 279 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/863 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1) `ZINC000119081421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119081421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081421 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 29, 31, 41, 29, 29, 29, 29, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 13, 13, 31, 31, 41, 41, 123, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 304 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119081421 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 Building ZINC000119081421 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119081421 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 862) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/862: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1) `ZINC000119081421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119081421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081421 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 31, 32, 39, 31, 31, 31, 31, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 13, 13, 32, 32, 39, 39, 117, 31, 31, 31, 31, 31, 31] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 279 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 863) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/863: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1) `ZINC000119081421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119081421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081421 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 29, 31, 41, 29, 29, 29, 29, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 3, 13, 13, 31, 31, 41, 41, 123, 29, 29, 29, 29, 29, 29] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 304 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119081421 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081421 Building ZINC000119081571 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119081571 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/864 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1) `ZINC000119081571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119081571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081571 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 30, 31, 41, 30, 30, 30, 30, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 14, 14, 31, 31, 41, 41, 123, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 294 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/865 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1) `ZINC000119081571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119081571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081571 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 3, 3, 3, 19, 30, 31, 38, 30, 30, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 3, 12, 12, 31, 31, 38, 38, 114, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119081571 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 Building ZINC000119081571 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119081571 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 864) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/864: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1) `ZINC000119081571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119081571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081571 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 22, 30, 31, 41, 30, 30, 30, 30, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 14, 14, 31, 31, 41, 41, 123, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 294 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 865) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/865: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1) `ZINC000119081571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119081571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000119081571 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 3, 3, 3, 19, 30, 31, 38, 30, 30, 30, 30, 4, 4, 4, 7, 7, 7, 7, 7, 4, 4, 4, 3, 12, 12, 31, 31, 38, 38, 114, 30, 30, 30, 30, 30, 30] 150 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 274 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119081571 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119081571 Building ZINC000119221581 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119221581 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/866 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119221581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221581 none CCOC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 22, 7, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 8, 3, 9, 13, 13, 13, 13, 13, 13, 31, 31, 31, 31, 31, 7, 7, 2, 3, 8, 8, 8, 8, 8, 3, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/867 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119221581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221581 none CCOC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 16, 11, 16, 9, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 11, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 9, 9, 2, 3, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119221581 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 Building ZINC000119221581 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119221581 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 866) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/866: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119221581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221581 none CCOC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 9, 22, 7, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 8, 3, 9, 13, 13, 13, 13, 13, 13, 31, 31, 31, 31, 31, 7, 7, 2, 3, 8, 8, 8, 8, 8, 3, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 867) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/867: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119221581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221581 none CCOC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 16, 11, 16, 9, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 11, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 9, 9, 2, 3, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221581 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119221581 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221581 Building ZINC000119221713 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119221713 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/868 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119221713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221713 none CCOC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 16, 11, 16, 9, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 11, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 9, 9, 2, 3, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/869 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119221713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221713 none CCOC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 9, 21, 7, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 10, 3, 9, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 7, 7, 2, 3, 10, 10, 10, 10, 10, 3, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119221713 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 Building ZINC000119221713 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119221713 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 868) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/868: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119221713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221713 none CCOC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 16, 16, 11, 16, 9, 11, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 7, 3, 11, 15, 15, 15, 15, 15, 15, 22, 22, 22, 22, 22, 9, 9, 2, 3, 7, 7, 7, 7, 7, 3, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 869) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/869: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1) `ZINC000119221713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119221713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119221713 none CCOC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 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, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 9, 21, 7, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 10, 3, 9, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 7, 7, 2, 3, 10, 10, 10, 10, 10, 3, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 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/335759/xcu-8058115.73/working/building/ZINC000119221713 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119221713 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119221713 Building ZINC000190008384 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190008384 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/870 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1) `ZINC000190008384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190008384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190008384 none Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 13, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/871 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1) `ZINC000190008384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190008384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190008384 none Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 15, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000190008384 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 Building ZINC000190008384 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190008384 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 870) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/870: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1) `ZINC000190008384.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190008384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190008384 none Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 13, 13, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 34, 34, 34, 34, 34, 34, 13, 13, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6, 34] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 871) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/871: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1) `ZINC000190008384.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190008384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000190008384 none Cn1cc([C@H]2OCC[C@@H]2NC(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 15, 15, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 15, 15, 15, 15, 2, 6, 6, 6, 6, 6, 6, 6, 31] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000190008384 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190008384 Building ZINC000119520714 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119520714 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/872 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1) `ZINC000119520714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119520714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119520714 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 1, 8, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 11, 14, 14, 14, 14, 14, 18, 18, 6, 6, 2, 2, 9, 9, 9, 9, 9, 2, 6, 6, 6, 6, 11, 11, 14, 14, 18, 6, 6, 6, 6, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/873 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1) `ZINC000119520714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119520714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119520714 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 1, 8, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 10, 14, 14, 14, 14, 14, 17, 17, 6, 6, 2, 2, 7, 7, 7, 7, 7, 2, 6, 6, 6, 6, 10, 10, 14, 14, 17, 6, 6, 6, 6, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119520714 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 Building ZINC000119520714 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119520714 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 872) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/872: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1) `ZINC000119520714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119520714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119520714 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 1, 8, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 11, 14, 14, 14, 14, 14, 18, 18, 6, 6, 2, 2, 9, 9, 9, 9, 9, 2, 6, 6, 6, 6, 11, 11, 14, 14, 18, 6, 6, 6, 6, 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 873) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/873: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1) `ZINC000119520714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119520714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000119520714 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(Cc3nccn3C(F)F)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 1, 8, 1, 1, 8, 5, 15, 15, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 1, 1, 1, 2, 4, 6, 6, 6, 6, 10, 14, 14, 14, 14, 14, 17, 17, 6, 6, 2, 2, 7, 7, 7, 7, 7, 2, 6, 6, 6, 6, 10, 10, 14, 14, 17, 6, 6, 6, 6, 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: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000119520714 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000119520714 Building ZINC000190068591 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190068591 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/874 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F) `ZINC000190068591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190068591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000190068591 none COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 13, 20, 20, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 6, 20, 20, 20, 31, 31, 31, 20, 20, 4, 10, 10, 10, 10, 10, 20] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/875 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F) `ZINC000190068591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190068591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000190068591 none COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 14, 20, 20, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 6, 20, 20, 20, 32, 32, 32, 20, 20, 4, 10, 10, 10, 10, 10, 20] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000190068591 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 Building ZINC000190068591 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000190068591 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 874) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/874: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F) `ZINC000190068591.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000190068591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000190068591 none COc1ccc(c2nsc(NC(=O)[C@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 13, 20, 20, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 6, 20, 20, 20, 31, 31, 31, 20, 20, 4, 10, 10, 10, 10, 10, 20] 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 875) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/875: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F) `ZINC000190068591.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000190068591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000190068591 none COc1ccc(c2nsc(NC(=O)[C@@]([O-])([SiH3])c3cnn(C)c3)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 14, 20, 20, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 6, 20, 20, 20, 32, 32, 32, 20, 20, 4, 10, 10, 10, 10, 10, 20] 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000190068591 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000190068591 Building ZINC000278995432 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278995432 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/876 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/876' -> `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)N1CC[C@]2(CNC(=O)C2)C1) `ZINC000278995432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278995432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995432 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/877 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/877' -> `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)N1CC[C@]2(CNC(=O)C2)C1) `ZINC000278995432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278995432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995432 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 1, 3, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000278995432 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 Building ZINC000278995432 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278995432 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 876) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/876: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1) `ZINC000278995432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278995432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995432 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 4, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 62 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 877) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/877: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1) `ZINC000278995432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278995432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995432 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 1, 1, 1, 1, 3, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 12, 12, 3, 12, 12, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000278995432 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995432 Building ZINC000278995434 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278995434 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/878 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/878' -> `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)N1CC[C@@]2(CNC(=O)C2)C1) `ZINC000278995434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278995434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995434 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/879 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/879' -> `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)N1CC[C@@]2(CNC(=O)C2)C1) `ZINC000278995434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278995434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995434 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000278995434 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 Building ZINC000278995434 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000278995434 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 878) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/878: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1) `ZINC000278995434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000278995434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995434 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 60 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 879) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/879: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1) `ZINC000278995434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000278995434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC000278995434 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@]2(CNC(=O)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 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, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 3, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 58 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000278995434 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000278995434 Building ZINC001621056623 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621056623 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/880 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1) `ZINC001621056623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621056623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001621056623 none Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 35, 35, 21, 21, 4, 2, 2, 2, 2, 2, 2, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/881 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1) `ZINC001621056623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621056623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001621056623 none Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 35, 35, 21, 21, 4, 2, 2, 2, 2, 2, 2, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001621056623 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 Building ZINC001621056623 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001621056623 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 880) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/880: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1) `ZINC001621056623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001621056623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001621056623 none Cc1cc(NCCNC(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 35, 35, 21, 21, 4, 2, 2, 2, 2, 2, 2, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 881) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/881: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1) `ZINC001621056623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001621056623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001621056623 none Cc1cc(NCCNC(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)n2ncnc2n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 35, 21, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 45, 35, 35, 21, 21, 4, 2, 2, 2, 2, 2, 2, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 187 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001621056623 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001621056623 Building ZINC000066858272 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000066858272 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/882 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1) `ZINC000066858272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000066858272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000066858272 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 40, 40, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 54, 55, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/883 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1) `ZINC000066858272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000066858272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000066858272 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 45, 45, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 54, 55, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000066858272 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 Building ZINC000066858272 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000066858272 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 882) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/882: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1) `ZINC000066858272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000066858272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000066858272 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 14, 40, 40, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 54, 55, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 147 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 883) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/883: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1) `ZINC000066858272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000066858272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC000066858272 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(CC(=O)N3CCN(C)CC3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 16, 45, 45, 50, 50, 50, 50, 50, 50, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 4, 4, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 54, 55, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 143 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000066858272 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000066858272 Building ZINC000279264759 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279264759 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/884 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)cn1) `ZINC000279264759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279264759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000279264759 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 3, 7, 11, 11, 11, 11, 11, 11, 11, 19, 19, 30, 30, 30, 30, 11, 11, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/885 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)cn1) `ZINC000279264759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279264759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000279264759 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 3, 8, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 30, 30, 12, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000279264759 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 Building ZINC000279264759 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000279264759 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 884) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/884: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)cn1) `ZINC000279264759.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000279264759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000279264759 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 3, 7, 11, 11, 11, 11, 11, 11, 11, 19, 19, 30, 30, 30, 30, 11, 11, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 30, 30, 11, 11, 11, 11, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 885) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/885: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)cn1) `ZINC000279264759.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000279264759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000279264759 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC23CCN(C(=O)OC(C)(C)C)CC3)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', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 3, 8, 12, 12, 12, 12, 12, 12, 12, 20, 20, 30, 30, 30, 30, 12, 12, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 12, 12, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000279264759 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000279264759 Building ZINC000563335940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563335940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/886 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000563335940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563335940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000563335940 none COCCNC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 15, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 33, 33, 15, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/887 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000563335940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563335940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000563335940 none COCCNC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 35, 35, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000563335940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 Building ZINC000563335940 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563335940 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 886) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/886: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000563335940.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563335940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000563335940 none COCCNC1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 15, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 4, 4, 50, 50, 50, 50, 50, 33, 33, 15, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 887) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/887: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCNC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000563335940.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563335940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 46 natoms 45 natoms 44 natoms 43 names: ZINC000563335940 none COCCNC1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 17, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 5, 50, 50, 50, 50, 50, 35, 35, 17, 5, 5, 5, 5, 5, 2, 2, 2, 2, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000563335940 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563335940 Building ZINC001129388288 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001129388288 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/888 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)cn1) `ZINC001129388288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001129388288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001129388288 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 2, 11, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/889 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)cn1) `ZINC001129388288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001129388288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001129388288 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 2, 11, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 10] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001129388288 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 Building ZINC001129388288 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001129388288 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 888) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/888: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)cn1) `ZINC001129388288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001129388288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001129388288 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 2, 11, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 11, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 889) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/889: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)cn1) `ZINC001129388288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001129388288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001129388288 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3cc(F)c(Br)cc32)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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'N.2', '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, 12, 1, 1, 1, 15, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 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] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 1, 1, 1, 2, 11, 18, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 10] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 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]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001129388288 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001129388288 Building ZINC001288093238 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288093238 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/890 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/890' -> `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]2C=C[C@H]1CC2) `ZINC001288093238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288093238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093238 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 14, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 15, 15, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/891 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/891' -> `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]2C=C[C@H]1CC2) `ZINC001288093238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288093238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093238 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 232 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288093238 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 Building ZINC001288093238 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288093238 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 890) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/890: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `ZINC001288093238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288093238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093238 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 14, 10, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 15, 15, 45, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 227 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 891) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/891: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `ZINC001288093238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288093238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093238 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 19, 14, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 232 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288093238 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093238 Building ZINC001288093239 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288093239 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/892 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/892' -> `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]2C=C[C@H]1CC2) `ZINC001288093239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288093239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093239 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/893 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/893' -> `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]2C=C[C@H]1CC2) `ZINC001288093239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288093239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093239 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 15, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 48, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 236 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288093239 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 Building ZINC001288093239 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288093239 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 892) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `ZINC001288093239.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288093239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093239 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 11, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 15, 15, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 219 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 893) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2) `ZINC001288093239.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288093239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001288093239 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@@H]2C=C[C@H]1CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 15, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 48, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 38, 39, 8, 41, 10, 11, 12, 13, 14, 15, 40, 44, 46, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 236 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288093239 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288093239 Building ZINC001288094796 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288094796 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/894 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/894' -> `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]1CC(C)(C)C) `ZINC001288094796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288094796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094796 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 48, 48, 48, 48, 48, 50, 50, 50, 50, 23, 23, 23, 20, 20, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 255 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/895 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/895' -> `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]1CC(C)(C)C) `ZINC001288094796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288094796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094796 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 48, 48, 48, 48, 48, 50, 50, 50, 50, 23, 23, 23, 18, 18, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 253 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288094796 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 Building ZINC001288094796 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288094796 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 894) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(C)(C)C) `ZINC001288094796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288094796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094796 none CN(C[C@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 15, 8, 15, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 31, 31, 48, 48, 48, 48, 48, 50, 50, 50, 50, 23, 23, 23, 20, 20, 45, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 255 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 895) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(C)(C)C) `ZINC001288094796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288094796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094796 none CN(C[C@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [23, 18, 11, 7, 12, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 34, 34, 48, 48, 48, 48, 48, 50, 50, 50, 50, 23, 23, 23, 18, 18, 36, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 253 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288094796 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094796 Building ZINC001288094798 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288094798 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/896 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/896' -> `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]1CC(C)(C)C) `ZINC001288094798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288094798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094798 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 48, 48, 48, 48, 48, 50, 50, 50, 50, 22, 22, 22, 17, 17, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/897 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/897' -> `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]1CC(C)(C)C) `ZINC001288094798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288094798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094798 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 48, 48, 48, 48, 48, 50, 50, 50, 50, 22, 22, 22, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 255 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288094798 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 Building ZINC001288094798 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288094798 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 896) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(C)(C)C) `ZINC001288094798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288094798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094798 none CN(C[C@@H](O)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 17, 10, 7, 11, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 34, 34, 48, 48, 48, 48, 48, 50, 50, 50, 50, 22, 22, 22, 17, 17, 33, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 244 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 897) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(C)(C)C) `ZINC001288094798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288094798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001288094798 none CN(C[C@@H](O)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1CC(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', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 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, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 48, 48, 48, 48, 48, 50, 50, 50, 50, 22, 22, 22, 19, 19, 42, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 150 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, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 255 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288094798 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288094798 Building ZINC000563401551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563401551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/898 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000563401551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563401551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000563401551 none Cn1cnnc1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 42, 24, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 37, 37, 32, 32, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/899 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000563401551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563401551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000563401551 none Cn1cnnc1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 41, 23, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 36, 36, 31, 31, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000563401551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 Building ZINC000563401551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000563401551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 898) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000563401551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000563401551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000563401551 none Cn1cnnc1CCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 42, 24, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 37, 37, 32, 32, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 899) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnnc1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000563401551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000563401551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000563401551 none Cn1cnnc1CCCNC(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 41, 23, 20, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 3, 48, 48, 48, 48, 36, 36, 31, 31, 20, 20, 4, 3, 3, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000563401551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000563401551 Building ZINC000470242568 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470242568 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/900 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000470242568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470242568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000470242568 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 11, 1, 17, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/901 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/901' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000470242568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470242568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000470242568 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 25, 25, 25, 10, 2, 15, 1, 1, 1, 2, 2, 1, 2, 2, 2, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470242568 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 Building ZINC000470242568 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470242568 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 900) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000470242568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470242568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000470242568 none CCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 11, 1, 17, 1, 1, 1, 2, 2, 1, 2, 2, 2, 26, 26, 26, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 2, 2, 2, 2, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 901) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O) `ZINC000470242568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470242568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 41 natoms 40 natoms 39 natoms 38 names: ZINC000470242568 none CCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 25, 25, 25, 25, 25, 10, 2, 15, 1, 1, 1, 2, 2, 1, 2, 2, 2, 25, 25, 25, 50, 50, 50, 50, 50, 25, 25, 25, 25, 25, 25, 2, 2, 2, 2, 25, 25] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470242568 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470242568 Building ZINC000180303864 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180303864 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/902 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1Br) `ZINC000180303864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180303864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000180303864 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 33, 13, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 13, 2, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/903 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1Br) `ZINC000180303864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180303864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000180303864 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 34, 14, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 34, 34, 34, 14, 2, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180303864 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 Building ZINC000180303864 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180303864 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 902) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1Br) `ZINC000180303864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180303864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000180303864 none COC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 33, 13, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 13, 13, 13, 13, 33, 33, 33, 13, 2, 6, 6, 6, 6, 6, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 903) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/903: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1Br) `ZINC000180303864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180303864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000180303864 none COC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)ccc1Br NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 17, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 34, 14, 14, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 14, 14, 14, 14, 34, 34, 34, 14, 2, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180303864 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180303864 Building ZINC000180390788 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390788 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/904 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/905 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/906 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/906' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/907 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/907' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390788 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 Building ZINC000180390788 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390788 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 904) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 905) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 906) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 907) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390788 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 Building ZINC000180390788 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390788 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 904) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 905) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 906) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 907) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390788 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 Building ZINC000180390788 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390788 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 904) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/904: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 905) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/905: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 30, 9, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 30, 30, 30, 13, 13, 9, 9, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 906) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/906: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 907) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/907: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1) `ZINC000180390788.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390788 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 14, 29, 12, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 29, 29, 29, 14, 14, 12, 12, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390788 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390788 Building ZINC000180390807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/908 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/909 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/909' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/910 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/910' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/911 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/911' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 Building ZINC000180390807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 908) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 909) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 910) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 911) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 Building ZINC000180390807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 908) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 909) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 910) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 911) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 Building ZINC000180390807 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000180390807 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 908) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/908: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 909) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/909: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 13, 28, 9, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 13, 13, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 910) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/910: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 911) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1) `ZINC000180390807.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000180390807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000180390807 none COC(=O)CCN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 12, 1, 11, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 27, 8, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 27, 27, 27, 12, 12, 8, 8, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180390807 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180390807 Building ZINC001350980765 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001350980765 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/912 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/913 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/913' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/914 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/914' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/915 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/915' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350980765 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 Building ZINC001350980765 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001350980765 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 912) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 913) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 914) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 915) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350980765 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 Building ZINC001350980765 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001350980765 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 912) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 913) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 914) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 915) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350980765 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 Building ZINC001350980765 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001350980765 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 912) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 913) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 33, 49, 33, 33, 33, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 33, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 152 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 914) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 915) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/915: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C) `ZINC001350980765.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001350980765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001350980765 none C[C@@H]1[C@H](C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)CCN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 36, 49, 36, 36, 36, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 36, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 148 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350980765 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350980765 Building ZINC000180525626 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180525626 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/916 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O) `ZINC000180525626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180525626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000180525626 none Cn1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 27, 17, 27, 27, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 35, 35, 35, 35, 35, 35, 27, 27, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/917 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O) `ZINC000180525626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180525626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000180525626 none Cn1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 25, 18, 25, 25, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 33, 33, 33, 33, 33, 33, 25, 25, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180525626 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 Building ZINC000180525626 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000180525626 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 916) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/916: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O) `ZINC000180525626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000180525626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000180525626 none Cn1cnn(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 27, 17, 27, 27, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 35, 35, 35, 35, 35, 35, 27, 27, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 917) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O) `ZINC000180525626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000180525626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000180525626 none Cn1cnn(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc4c(c3)CCC4)cc2)c1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', '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, 8, 1, 8, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 25, 18, 25, 25, 5, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 33, 33, 33, 33, 33, 33, 25, 25, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000180525626 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000180525626 Building ZINC000470483095 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470483095 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/918 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1scnc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000470483095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470483095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470483095 none COCCN(Cc1scnc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 14, 1, 8, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 10, 4, 2, 4, 10, 17, 17, 17, 17, 17, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 14, 14, 10, 10, 10, 10, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/919 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1scnc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000470483095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470483095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470483095 none COCCN(Cc1scnc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 14, 1, 8, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 10, 4, 2, 4, 9, 17, 17, 17, 17, 17, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 14, 14, 10, 10, 9, 9, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470483095 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 Building ZINC000470483095 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470483095 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 918) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1scnc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000470483095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470483095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470483095 none COCCN(Cc1scnc1C)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 14, 1, 8, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 10, 4, 2, 4, 10, 17, 17, 17, 17, 17, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 14, 14, 10, 10, 10, 10, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 919) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1scnc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000470483095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470483095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000470483095 none COCCN(Cc1scnc1C)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 14, 1, 8, 1, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 14, 10, 4, 2, 4, 9, 17, 17, 17, 17, 17, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 14, 14, 10, 10, 9, 9, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470483095 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470483095 Building ZINC000565166130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565166130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/920 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565166130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166130 none CCOC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/921 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565166130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166130 none CCOC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565166130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 Building ZINC000565166130 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565166130 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 920) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565166130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166130 none CCOC(=O)[C@@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 17, 17, 17, 17] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 921) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565166130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166130 none CCOC(=O)[C@@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 8, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 5, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 5, 5, 5, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565166130 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166130 Building ZINC000565166133 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565166133 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/922 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565166133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166133 none CCOC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/923 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565166133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166133 none CCOC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 5, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 5, 5, 5, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565166133 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 Building ZINC000565166133 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565166133 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 922) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565166133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166133 none CCOC(=O)[C@](C)(NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 5, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 5, 5, 5, 3, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 923) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1) `ZINC000565166133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565166133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000565166133 none CCOC(=O)[C@](C)(NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', '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.3', 'C.3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 5, 9, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 5, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 5, 5, 5, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 16, 16, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565166133 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565166133 Building ZINC000470580846 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470580846 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/924 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1) `ZINC000470580846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470580846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580846 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 8, 8, 8, 8, 8, 22, 22, 22, 15, 15, 8, 8, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/925 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1) `ZINC000470580846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470580846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580846 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 9, 9, 9, 9, 9, 19, 19, 19, 14, 14, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470580846 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 Building ZINC000470580846 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470580846 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 924) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1) `ZINC000470580846.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470580846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580846 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 8, 8, 8, 8, 8, 22, 22, 22, 15, 15, 8, 8, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 925) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/925: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1) `ZINC000470580846.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470580846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580846 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 9, 9, 9, 9, 9, 19, 19, 19, 14, 14, 7, 7, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 95 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470580846 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580846 Building ZINC000470580847 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470580847 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/926 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1) `ZINC000470580847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470580847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580847 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 21, 15, 15, 8, 8, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/927 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1) `ZINC000470580847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470580847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580847 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 7, 7, 7, 7, 7, 22, 22, 22, 15, 15, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470580847 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 Building ZINC000470580847 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470580847 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 926) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/926: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1) `ZINC000470580847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470580847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580847 none COCCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 5, 10, 10, 10, 10, 10, 21, 21, 21, 15, 15, 8, 8, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 104 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 927) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1) `ZINC000470580847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470580847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000470580847 none COCCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 8, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 7, 7, 7, 7, 7, 22, 22, 22, 15, 15, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470580847 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470580847 Building ZINC000470585099 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470585099 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/928 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1ccnn1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000470585099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470585099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000470585099 none COCCN(Cc1ccnn1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 10, 10, 8, 8, 7, 7, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/929 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1ccnn1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000470585099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470585099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000470585099 none COCCN(Cc1ccnn1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 10, 10, 8, 8, 7, 7, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470585099 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 Building ZINC000470585099 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470585099 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 928) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1ccnn1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000470585099.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470585099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000470585099 none COCCN(Cc1ccnn1C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 10, 10, 8, 8, 7, 7, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 929) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/929: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(Cc1ccnn1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000470585099.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470585099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000470585099 none COCCN(Cc1ccnn1C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 8, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 10, 8, 3, 2, 3, 7, 14, 14, 14, 14, 14, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 10, 10, 8, 8, 7, 7, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470585099 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470585099 Building ZINC000470650624 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470650624 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/930 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000470650624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470650624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000470650624 none CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 34, 48, 34, 34, 34, 18, 1, 26, 1, 1, 1, 4, 4, 1, 4, 4, 4, 34, 34, 48, 48, 48, 48, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/931 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000470650624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470650624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000470650624 none CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 40, 48, 40, 40, 40, 18, 1, 27, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 48, 48, 48, 48, 40, 40, 40, 40, 4, 4, 4, 4, 40, 40, 40, 40] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470650624 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 Building ZINC000470650624 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470650624 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 930) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/930: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000470650624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470650624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000470650624 none CNC(=O)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 34, 48, 34, 34, 34, 18, 1, 26, 1, 1, 1, 4, 4, 1, 4, 4, 4, 34, 34, 48, 48, 48, 48, 34, 34, 34, 34, 4, 4, 4, 4, 34, 34, 34, 34] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 140 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 931) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1) `ZINC000470650624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470650624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000470650624 none CNC(=O)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 5, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 40, 48, 40, 40, 40, 18, 1, 27, 1, 1, 1, 4, 4, 1, 1, 4, 4, 40, 40, 48, 48, 48, 48, 40, 40, 40, 40, 4, 4, 4, 4, 40, 40, 40, 40] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 118 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470650624 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470650624 Building ZINC000470754270 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470754270 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/932 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O) `ZINC000470754270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470754270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000470754270 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 14, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 6, 6, 6, 31, 31, 31, 22, 22, 14, 14, 6, 6, 6, 6, 6, 6, 2, 2, 5, 5, 5, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/933 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O) `ZINC000470754270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470754270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000470754270 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 13, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 29, 29, 29, 20, 20, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 2, 5, 5] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470754270 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 Building ZINC000470754270 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470754270 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 932) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O) `ZINC000470754270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470754270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000470754270 none COCCN1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 14, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 6, 6, 6, 31, 31, 31, 22, 22, 14, 14, 6, 6, 6, 6, 6, 6, 2, 2, 5, 5, 5, 2, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 933) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O) `ZINC000470754270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470754270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC000470754270 none COCCN1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(OC)c(Cl)c2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', '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', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', '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'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 13, 5, 5, 5, 5, 5, 4, 2, 4, 1, 1, 1, 2, 2, 2, 2, 5, 2, 2, 2, 5, 5, 5, 29, 29, 29, 20, 20, 13, 13, 5, 5, 5, 5, 5, 5, 2, 2, 5, 5, 5, 2, 5, 5] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470754270 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470754270 Building ZINC000470766911 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470766911 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/934 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470766911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766911 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 5, 18, 18, 18, 18, 18, 12, 12, 12, 3, 4, 4, 8, 8, 8, 4, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/935 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470766911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766911 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 4, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 16, 16, 16, 16, 16, 10, 10, 10, 2, 4, 4, 9, 9, 9, 4, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470766911 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 Building ZINC000470766911 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470766911 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 934) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766911.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470766911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766911 none COC(=O)[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 3, 4, 8, 4, 4, 4, 5, 18, 18, 18, 18, 18, 12, 12, 12, 3, 4, 4, 8, 8, 8, 4, 18, 18, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 935) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766911.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470766911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766911 none COC(=O)[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 4, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 9, 4, 4, 4, 4, 16, 16, 16, 16, 16, 10, 10, 10, 2, 4, 4, 9, 9, 9, 4, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470766911 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766911 Building ZINC000470766921 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470766921 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/936 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470766921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766921 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 4, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 16, 16, 16, 16, 16, 10, 10, 10, 2, 4, 4, 8, 8, 8, 4, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/937 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470766921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766921 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 5, 17, 17, 17, 17, 17, 12, 12, 12, 3, 4, 4, 8, 8, 8, 4, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470766921 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 Building ZINC000470766921 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470766921 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 936) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766921.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470766921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766921 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 4, 10, 2, 4, 2, 1, 2, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 4, 16, 16, 16, 16, 16, 10, 10, 10, 2, 4, 4, 8, 8, 8, 4, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 937) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1) `ZINC000470766921.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470766921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC000470766921 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(OC)c(Cl)c1)c1ccn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 1, 8, 5, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 5, 12, 3, 5, 3, 1, 3, 1, 1, 1, 4, 4, 2, 4, 8, 4, 4, 4, 5, 17, 17, 17, 17, 17, 12, 12, 12, 3, 4, 4, 8, 8, 8, 4, 17, 17, 17, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470766921 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470766921 Building ZINC000282123601 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282123601 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/938 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/938' -> `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)N1CC(=O)N(C)[C@H](C)C1) `ZINC000282123601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282123601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123601 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/939 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/939' -> `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)N1CC(=O)N(C)[C@H](C)C1) `ZINC000282123601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282123601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123601 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 1, 1, 1, 2, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282123601 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 Building ZINC000282123601 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282123601 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 938) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1) `ZINC000282123601.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282123601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123601 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 2, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 939) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1) `ZINC000282123601.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282123601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123601 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 7, 15, 15, 4, 4, 1, 1, 1, 2, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 15, 15, 15, 15, 15, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282123601 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123601 Building ZINC000282123604 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282123604 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/940 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/940' -> `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)N1CC(=O)N(C)[C@@H](C)C1) `ZINC000282123604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282123604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 10, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/941 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/941' -> `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)N1CC(=O)N(C)[C@@H](C)C1) `ZINC000282123604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282123604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 2, 13, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282123604 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 Building ZINC000282123604 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000282123604 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 940) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1) `ZINC000282123604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282123604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123604 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 1, 1, 1, 2, 10, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 15, 15, 4, 15, 15, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 73 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 941) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/941: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1) `ZINC000282123604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282123604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000282123604 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC(=O)N(C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 1, 1, 1, 2, 13, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 11, 11, 6, 11, 11, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282123604 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282123604 Building ZINC000565441896 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565441896 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/942 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000565441896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565441896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000565441896 none CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 10, 27, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 10, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/943 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000565441896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565441896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000565441896 none CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 10, 27, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 10, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565441896 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 Building ZINC000565441896 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565441896 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 942) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/942: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000565441896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565441896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000565441896 none CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 10, 27, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 10, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 943) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/943: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1) `ZINC000565441896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565441896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000565441896 none CN(C)S(=O)(=O)c1cccc(CNC(=O)[C@]([O-])([SiH3])c2ccc(F)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 27, 50, 50, 27, 10, 27, 23, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 27, 50, 50, 50, 50, 50, 50, 10, 27, 27, 10, 10, 2, 2, 2, 2, 2, 27] 50 rigid atoms, others: [13, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565441896 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565441896 Building ZINC000470914746 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470914746 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/944 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O) `ZINC000470914746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470914746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000470914746 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 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, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 8, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 27, 27, 48, 48, 48, 23, 23, 23, 8, 4, 4, 4, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/945 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O) `ZINC000470914746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470914746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000470914746 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 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, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 8, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 23, 23, 26, 26, 49, 49, 49, 23, 23, 23, 8, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470914746 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 Building ZINC000470914746 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470914746 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 944) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/944: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O) `ZINC000470914746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470914746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000470914746 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 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, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 8, 4, 1, 4, 1, 1, 1, 4, 4, 1, 1, 4, 4, 23, 23, 27, 27, 48, 48, 48, 23, 23, 23, 8, 4, 4, 4, 4, 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 945) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/945: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O) `ZINC000470914746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470914746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000470914746 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 11, 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, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 23, 23, 23, 23, 8, 4, 1, 4, 1, 1, 1, 4, 4, 1, 4, 4, 4, 23, 23, 26, 26, 49, 49, 49, 23, 23, 23, 8, 4, 4, 4, 4, 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470914746 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470914746 Building ZINC000470916113 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470916113 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/946 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O) `ZINC000470916113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470916113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000470916113 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 14, 14, 27, 27, 27, 8, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/947 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O) `ZINC000470916113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470916113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000470916113 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 9, 9, 16, 16, 33, 33, 33, 9, 9, 9, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470916113 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 Building ZINC000470916113 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470916113 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 946) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/946: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O) `ZINC000470916113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470916113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000470916113 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 9, 9, 9, 5, 8, 8, 14, 14, 27, 27, 27, 8, 8, 8, 2, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 947) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/947: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O) `ZINC000470916113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470916113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000470916113 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 9, 9, 16, 16, 33, 33, 33, 9, 9, 9, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 16, 16] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470916113 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916113 Building ZINC000470916728 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470916728 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/948 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O) `ZINC000470916728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470916728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000470916728 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', '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, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 14, 14, 14, 14, 14, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 26, 26, 26, 14, 14, 14, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/949 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O) `ZINC000470916728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470916728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000470916728 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', '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, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 27, 27, 27, 14, 14, 14, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470916728 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 Building ZINC000470916728 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000470916728 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 948) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/948: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O) `ZINC000470916728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000470916728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000470916728 none CSc1nn(C)c(NC(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', '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, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 14, 14, 14, 14, 14, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 26, 26, 26, 14, 14, 14, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 949) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/949: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O) `ZINC000470916728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000470916728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000470916728 none CSc1nn(C)c(NC(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.am', '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, 14, 1, 8, 8, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 7, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 27, 27, 27, 14, 14, 14, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000470916728 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000470916728 Building ZINC001350989351 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350989351 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/950 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1) `ZINC001350989351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350989351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001350989351 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 20, 20, 21, 21, 21, 21, 11, 11, 11, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/951 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1) `ZINC001350989351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350989351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001350989351 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 19, 19, 21, 21, 21, 21, 10, 10, 10, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350989351 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 Building ZINC001350989351 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001350989351 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 950) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/950: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1) `ZINC001350989351.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001350989351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001350989351 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 11, 11, 11, 11, 11, 11, 20, 20, 21, 21, 21, 21, 11, 11, 11, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 951) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/951: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1) `ZINC001350989351.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001350989351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 55 natoms 54 natoms 53 natoms 52 names: ZINC001350989351 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)[C@@H]2[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 4, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 10, 10, 10, 10, 19, 19, 21, 21, 21, 21, 10, 10, 10, 4, 4, 9, 9, 9, 9, 9, 4, 5, 5, 5, 10, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 10, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001350989351 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001350989351 Building ZINC000565562372 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562372 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/952 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562372 none O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 17, 17, 17, 17, 46, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/953 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562372 none O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 19, 19, 19, 19, 45, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 33, 33, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562372 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 Building ZINC000565562372 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562372 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 952) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/952: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562372.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562372 none O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 17, 17, 17, 17, 46, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 2, 2, 17, 17, 35, 35, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 953) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/953: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562372.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562372 none O=C(N1C[C@@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 19, 19, 19, 19, 45, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 33, 33, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562372 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562372 Building ZINC000565562373 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562373 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/954 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562373 none O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 44, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/955 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562373 none O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 15, 15, 15, 15, 44, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562373 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 Building ZINC000565562373 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562373 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 954) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/954: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562373 none O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 44, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 34, 34, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 955) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/955: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562373 none O=C(N1C[C@H](C[C@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 15, 15, 15, 15, 44, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 1, 1, 1, 3, 3, 1, 3, 3, 15, 15, 33, 33, 50, 50, 50, 50, 50, 15, 15, 15, 15, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 147 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562373 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562373 Building ZINC000565562374 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562374 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/956 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562374 none O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 43, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 3, 3, 1, 3, 3, 14, 14, 33, 33, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/957 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562374 none O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 44, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 35, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562374 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 Building ZINC000565562374 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562374 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 956) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/956: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562374 none O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 8, 14, 14, 14, 14, 43, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 14, 14, 1, 1, 1, 3, 3, 1, 3, 3, 14, 14, 33, 33, 50, 50, 50, 50, 50, 14, 14, 14, 14, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 150 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 957) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562374 none O=C(N1C[C@@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 12, 12, 12, 12, 44, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 12, 12, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 35, 35, 50, 50, 50, 50, 50, 12, 12, 12, 12, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562374 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562374 Building ZINC000565562375 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562375 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/958 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562375 none O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 18, 18, 18, 18, 44, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 1, 1, 1, 3, 3, 1, 3, 3, 18, 18, 32, 32, 50, 50, 50, 50, 50, 18, 18, 18, 18, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/959 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562375 none O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 16, 16, 16, 16, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 1, 2, 2, 16, 16, 34, 34, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562375 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 Building ZINC000565562375 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000565562375 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 958) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1) `ZINC000565562375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000565562375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562375 none O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 18, 18, 18, 18, 44, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 1, 1, 1, 3, 3, 1, 3, 3, 18, 18, 32, 32, 50, 50, 50, 50, 50, 18, 18, 18, 18, 3, 3, 1, 3, 3] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 959) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000565562375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000565562375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000565562375 none O=C(N1C[C@H](C[C@@H]2COCC(=O)N2)c2ccccc21)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 9, 16, 16, 16, 16, 45, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 1, 1, 1, 2, 2, 1, 2, 2, 16, 16, 34, 34, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 2, 1, 2, 2] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 148 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000565562375 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000565562375 Building ZINC000471137004 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471137004 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/960 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F) `ZINC000471137004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471137004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000471137004 none Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 12, 8, 12, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/961 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F) `ZINC000471137004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471137004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000471137004 none Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 30 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471137004 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 Building ZINC000471137004 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471137004 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 960) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F) `ZINC000471137004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471137004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000471137004 none Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 12, 8, 12, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 24, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 41 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 63 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 961) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/961: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F) `ZINC000471137004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471137004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000471137004 none Cc1nn(C)c(C)c1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C)C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'H', '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', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 7, 4, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 30 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471137004 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471137004 Building ZINC001288141550 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141550 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/962 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141550 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 48, 48, 48, 48, 48, 50, 50, 21, 21, 21, 21, 21, 39, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 48, 48, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/963 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141550 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 49, 49, 49, 49, 49, 50, 50, 20, 20, 20, 20, 20, 39, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141550 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 Building ZINC001288141550 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141550 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 962) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/962: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141550 none CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 21, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 48, 48, 48, 48, 48, 50, 50, 21, 21, 21, 21, 21, 39, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 48, 48, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 963) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141550 none CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 13, 7, 13, 13, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 49, 49, 49, 49, 49, 50, 50, 20, 20, 20, 20, 20, 39, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 232 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141550 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141550 Building ZINC001288141551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/964 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141551 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 20, 20, 20, 49, 49, 49, 49, 49, 50, 50, 18, 18, 18, 18, 18, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 228 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/965 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141551 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 12, 6, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 24, 49, 49, 49, 49, 49, 50, 50, 20, 20, 20, 20, 20, 36, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 238 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 Building ZINC001288141551 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141551 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 964) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141551 none CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 12, 7, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 18, 20, 20, 20, 49, 49, 49, 49, 49, 50, 50, 18, 18, 18, 18, 18, 36, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 228 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 965) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/965: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1) `ZINC001288141551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141551 none CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1C[C@H]1C1CC1 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.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 20, 12, 6, 12, 12, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 24, 24, 24, 49, 49, 49, 49, 49, 50, 50, 20, 20, 20, 20, 20, 36, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 49, 49, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 238 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141551 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141551 Building ZINC001288141734 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141734 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/966 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141734 none CN(C[C@@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 45, 45, 45, 45, 45, 50, 50, 50, 22, 22, 22, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/967 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141734 none CN(C[C@@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 8, 5, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 30, 30, 44, 44, 44, 44, 45, 50, 50, 50, 17, 17, 17, 12, 12, 24, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141734 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 Building ZINC001288141734 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141734 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 966) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/966: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141734 none CN(C[C@@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 45, 45, 45, 45, 45, 50, 50, 50, 22, 22, 22, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 233 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 967) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/967: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141734 none CN(C[C@@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 8, 5, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 17, 30, 30, 44, 44, 44, 44, 45, 50, 50, 50, 17, 17, 17, 12, 12, 24, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 231 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141734 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141734 Building ZINC001288141735 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141735 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/968 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141735 none CN(C[C@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 8, 5, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 30, 45, 45, 45, 45, 46, 50, 50, 50, 20, 20, 20, 13, 13, 24, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/969 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141735 none CN(C[C@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 43, 43, 43, 43, 44, 50, 50, 50, 21, 21, 21, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141735 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 Building ZINC001288141735 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001288141735 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 968) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/968: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141735.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001288141735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141735 none CN(C[C@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 8, 5, 8, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 30, 45, 45, 45, 45, 46, 50, 50, 50, 20, 20, 20, 13, 13, 24, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 229 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 969) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1C[C@H]1C1CCC1) `ZINC001288141735.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001288141735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001288141735 none CN(C[C@H](O)CN(C)C(=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.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 10, 7, 10, 10, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 21, 27, 27, 43, 43, 43, 43, 44, 50, 50, 50, 21, 21, 21, 15, 15, 30, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [45, 43, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 46, 41, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 236 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001288141735 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001288141735 Building ZINC000282477469 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282477469 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/970 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/971 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/972 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/972' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/973 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/973' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282477469 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 Building ZINC000282477469 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282477469 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 970) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 971) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 972) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 973) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282477469 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 Building ZINC000282477469 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282477469 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 970) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 971) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 972) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 973) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282477469 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 Building ZINC000282477469 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000282477469 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 970) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 971) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 972) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 4, 4, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32, 31, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 32, 32, 32, 32, 32, 32, 32, 9, 9, 9, 9, 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, 45, 46]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 973) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N2CCC(N3CCc4cc(F)ccc43)CC2)cn1) `ZINC000282477469.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000282477469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000282477469 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCC(N3CCc4cc(F)ccc43)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.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 1, 1, 1, 15, 1, 1, 1, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7] 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]) total number of confs: 46 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000282477469 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000282477469 Building ZINC000471511691 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471511691 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/974 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471511691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511691 none COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 13, 32, 13, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 35 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/975 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471511691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511691 none COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 14, 31, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 2, 3, 3, 31, 31, 31, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3] 34 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471511691 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 Building ZINC000471511691 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471511691 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 974) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471511691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511691 none COC(=O)[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 13, 32, 13, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 35 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]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 975) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/975: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471511691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511691 none COC(=O)[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 14, 31, 14, 14, 14, 14, 14, 14, 9, 1, 9, 1, 1, 1, 3, 3, 1, 2, 3, 3, 31, 31, 31, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3] 34 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471511691 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511691 Building ZINC000471511692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471511692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/976 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471511692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511692 none COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 15, 32, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3] 34 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/977 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471511692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511692 none COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 13, 33, 13, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 33, 33, 33, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 36 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471511692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 Building ZINC000471511692 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471511692 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 976) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/976: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471511692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511692 none COC(=O)[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 15, 32, 15, 15, 15, 15, 15, 15, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 3, 3, 32, 32, 32, 15, 15, 15, 15, 15, 15, 3, 3, 3, 3] 34 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 977) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/977: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471511692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471511692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000471511692 none COC(=O)[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 13, 33, 13, 13, 13, 13, 13, 13, 9, 1, 9, 1, 1, 1, 3, 3, 1, 3, 3, 3, 33, 33, 33, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3] 36 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]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471511692 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471511692 Building ZINC000471704183 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471704183 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/978 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471704183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471704183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000471704183 none O=C(NCc1nnnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 25, 25, 25, 25, 37, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/979 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471704183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471704183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000471704183 none O=C(NCc1nnnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 25, 25, 25, 25, 25, 41, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 3, 16, 16, 41, 41, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471704183 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 Building ZINC000471704183 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000471704183 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 978) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/978: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471704183.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471704183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000471704183 none O=C(NCc1nnnn1CC1CC1)[C@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 25, 25, 25, 25, 25, 37, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 3, 15, 15, 37, 37, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 979) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/979: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nnnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1) `ZINC000471704183.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471704183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000471704183 none O=C(NCc1nnnn1CC1CC1)[C@@]([O-])([SiH3])c1ccc(Br)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 8, 8, 8, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 25, 25, 25, 25, 25, 41, 50, 50, 1, 1, 1, 2, 2, 1, 2, 2, 2, 3, 16, 16, 41, 41, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471704183 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471704183 Building ZINC000471751317 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000471751317 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/980 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/981 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/982 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/982' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/983 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/983' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471751317 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 Building ZINC000471751317 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000471751317 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 980) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 981) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 982) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 983) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471751317 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 Building ZINC000471751317 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000471751317 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 980) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 981) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 982) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 983) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471751317 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 Building ZINC000471751317 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000471751317 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 980) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/980: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 981) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/981: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 31, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 101 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `2' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 2 (index: 982) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/982: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `3' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 3 (index: 983) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1) `ZINC000471751317.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000471751317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000471751317 none CC[N@]1CC[N@@](c2ccc(CNC(=O)[C@]([O-])([SiH3])c3ccccc3)cn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 8, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 32, 16, 16, 16, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 6, 6, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50] 50 rigid atoms, others: [43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49]) total number of confs: 102 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000471751317 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/0.* 2: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/2.* 3: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/3.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000471751317 Building ZINC001526794078 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526794078 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/984 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)n1) `ZINC001526794078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526794078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526794078 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/985 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)n1) `ZINC001526794078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526794078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526794078 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526794078 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 Building ZINC001526794078 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001526794078 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 984) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)n1) `ZINC001526794078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001526794078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526794078 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 985) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)n1) `ZINC001526794078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001526794078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001526794078 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cnn(C)c2)c(C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 16, 16, 46, 46, 46, 46, 46, 16, 16, 16] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 82 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001526794078 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001526794078 Building ZINC001351007096 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007096 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/986 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007096 none O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 21, 10, 10, 10, 23, 33, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 21, 21, 63, 23, 23, 33, 33, 99, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/987 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007096 none O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 24, 10, 10, 10, 19, 28, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 24, 24, 72, 19, 19, 28, 28, 84, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 334 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007096 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 Building ZINC001351007096 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007096 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 986) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007096 none O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 21, 10, 10, 10, 23, 33, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 21, 21, 63, 23, 23, 33, 33, 99, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 987) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/987: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007096 none O=C(N1C[C@@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 24, 10, 10, 10, 19, 28, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 24, 24, 72, 19, 19, 28, 28, 84, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 334 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007096 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007096 Building ZINC001351007097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/988 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007097 none O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 23, 10, 10, 10, 20, 30, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 23, 23, 69, 20, 20, 30, 30, 90, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/989 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007097 none O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 11, 11, 11, 11, 21, 11, 11, 11, 24, 34, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 21, 21, 63, 24, 24, 34, 34, 102, 11, 11, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 Building ZINC001351007097 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007097 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 988) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/988: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007097 none O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 10, 10, 10, 10, 23, 10, 10, 10, 20, 30, 10, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 23, 23, 69, 20, 20, 30, 30, 90, 10, 10, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 343 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 989) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/989: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007097 none O=C(N1C[C@H](CO)[C@@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 11, 11, 11, 11, 21, 11, 11, 11, 24, 34, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 21, 21, 63, 24, 24, 34, 34, 102, 11, 11, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 344 number of broken/clashed sets: 105 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007097 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007097 Building ZINC001351007127 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007127 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/990 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007127 none O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 11, 11, 11, 11, 22, 11, 11, 11, 27, 35, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 22, 22, 66, 27, 27, 35, 35, 105, 11, 11, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 365 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/991 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007127 none O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 4, 11, 11, 11, 11, 19, 11, 11, 11, 23, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 19, 19, 57, 23, 23, 36, 36, 108, 11, 11, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 354 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007127 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 Building ZINC001351007127 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001351007127 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 990) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/990: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007127.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001351007127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007127 none O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 3, 11, 11, 11, 11, 22, 11, 11, 11, 27, 35, 11, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 22, 22, 66, 27, 27, 35, 35, 105, 11, 11, 3, 3] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 365 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 991) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/991: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001351007127.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001351007127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001351007127 none O=C(N1C[C@H](CO)[C@H](CCO)C1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 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] 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: [2, 1, 4, 11, 11, 11, 11, 19, 11, 11, 11, 23, 36, 11, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 19, 19, 57, 23, 23, 36, 36, 108, 11, 11, 4, 4] 450 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 354 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC001351007127 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC001351007127 Building ZINC000283110253 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000283110253 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/992 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000283110253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110253 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 24, 49, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/993 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000283110253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110253 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 27, 50, 50, 50, 50, 50, 50, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000283110253 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 Building ZINC000283110253 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000283110253 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 992) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/992: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000283110253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110253 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 24, 49, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 24, 24, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 993) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/993: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000283110253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110253 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 27, 50, 50, 50, 50, 50, 50, 11, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 11, 11, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000283110253 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110253 Building ZINC000283110257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000283110257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/994 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000283110257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110257 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 3, 10, 10, 10, 10, 10, 12, 12, 28, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/995 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000283110257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110257 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 3, 9, 9, 9, 9, 9, 11, 11, 26, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 9, 9, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000283110257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 Building ZINC000283110257 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000283110257 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 994) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/994: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000283110257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110257 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 3, 10, 10, 10, 10, 10, 12, 12, 28, 50, 50, 50, 50, 50, 50, 10, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 28, 28, 50, 50, 50, 50, 50, 10, 10, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 995) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/995: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1) `ZINC000283110257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000283110257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC000283110257 none Cc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)COc3ccccc3)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 3, 9, 9, 9, 9, 9, 11, 11, 26, 50, 50, 50, 50, 50, 50, 9, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 26, 26, 50, 50, 50, 50, 50, 9, 9, 2, 2] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000283110257 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000283110257 Building ZINC000472191951 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472191951 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/996 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)s1) `ZINC000472191951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472191951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000472191951 none CCOC(=O)c1cnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 30, 30, 30, 9, 9, 9, 9, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 50, 50, 50, 50, 50, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/997 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)s1) `ZINC000472191951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472191951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000472191951 none CCOC(=O)c1cnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 30, 30, 30, 12, 12, 12, 12, 6, 2, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 50, 50, 50, 50, 50, 30, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000472191951 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 Building ZINC000472191951 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472191951 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 996) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/996: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)s1) `ZINC000472191951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472191951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000472191951 none CCOC(=O)c1cnc(N2CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 30, 30, 30, 9, 9, 9, 9, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 50, 50, 50, 50, 50, 30, 9, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 13, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 997) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/997: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)s1) `ZINC000472191951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472191951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000472191951 none CCOC(=O)c1cnc(N2CCN(C(=O)[C@]([O-])([SiH3])c3ccccc3)CC2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 30, 50, 30, 30, 30, 12, 12, 12, 12, 6, 2, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 30, 50, 50, 50, 50, 50, 30, 12, 12, 12, 12, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000472191951 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472191951 Building ZINC000472199963 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472199963 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/998 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000472199963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472199963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000472199963 none NC(=O)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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: [8, 1, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 13, 13, 13, 13, 13, 13, 6, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 45, 45, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 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]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/999 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000472199963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472199963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000472199963 none NC(=O)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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: [8, 1, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 27, 45, 11, 11, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 45, 45, 27, 27, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11] 45 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]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000472199963 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 Building ZINC000472199963 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000472199963 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 998) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/998: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000472199963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472199963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000472199963 none NC(=O)C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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: [8, 1, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 13, 13, 13, 13, 13, 13, 6, 2, 8, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 50, 50, 45, 45, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 13, 13] 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]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 mkdir: created directory `1' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 1 (index: 999) grep: /scratch/xiaobo/335759/xcu-8058115.73/working/3D/999: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000472199963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000472199963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000472199963 none NC(=O)C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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: [8, 1, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 27, 45, 11, 11, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 45, 45, 27, 27, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11] 45 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]) total number of confs: 175 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000472199963 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/0.* 1: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963/1.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199963 Building ZINC000472199969 mkdir: created directory `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000472199969 mkdir: created directory `0' /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969/0 /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/335759/xcu-8058115.73/working/3D/1000 `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1) `ZINC000472199969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000472199969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000472199969 none NC(=O)C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)cc2)C1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', '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: [8, 1, 11, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 1, 1, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 46, 11, 11, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 3, 3, 1, 3, 3, 3, 11, 46, 46, 28, 28, 11, 11, 11, 11, 11, 11, 3, 3, 3, 3, 11, 11] 46 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]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969 /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Finished preparing ZINC000472199969 Recording results /scratch/xiaobo/335759/xcu-8058115.73/working /scratch/xiaobo/335759/xcu-8058115.73 Appending to /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.* 0: /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969/0.* Removing working files in /scratch/xiaobo/335759/xcu-8058115.73/working/building/ZINC000472199969 /scratch/xiaobo/335759/xcu-8058115.73 Compressing combined databse files /scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/335759/xcu-8058115.73/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/335759/xcu-8058115.73/working/3D/1001' removed directory: `/scratch/xiaobo/335759/xcu-8058115.73/working/3D' rmdir: removing directory, `/scratch/xiaobo/335759/xcu-8058115.73/working/building' rmdir: removing directory, `/scratch/xiaobo/335759/xcu-8058115.73/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/logs `/scratch/xiaobo/335759/xcu-8058115.73' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xcu' `/scratch/xiaobo/335759/xcu-8058115.73/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xcu/finished' `/scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xbc/outputs/xcu/finished/xcu.db2.gz' removed `/scratch/xiaobo/335759/xcu-8058115.73/finished/xcu.db2.gz' removed directory: `/scratch/xiaobo/335759/xcu-8058115.73/finished' removed directory: `/scratch/xiaobo/335759/xcu-8058115.73'